#list name reference description total probes expected actual enrichment bin prob analysis_name histone deacetylase complex GO:0000118 Complex that possesses histone deacetylase activity. 41 0.101349681119296 0 0 1 M02A.profile.d50 mediator complex GO:0000119 A protein complex that enables the RNA polymerase II-general RNA polymerase II transcription factor complex to react to transcriptional activator proteins; also enhances the level of basal transcription. 17 0.0420230385128788 1 23.7964705882353 0.0412021928988779 M02A.profile.d50 histone acetyltransferase complex GO:0000123 Complex that possesses histone acetyltransferase activity. 17 0.0420230385128788 0 0 1 M02A.profile.d50 Golgi membrane GO:0000139 The lipid bilayer surrounding any of the compartments of the Golgi apparatus. 188 0.464725367083601 1 2.1518085106383 0.372053748413572 M02A.profile.d50 ubiquitin ligase complex GO:0000151 A protein complex that includes a ubiquitin-protein ligase (E3) and other proteins that may confer substrate specificity on the complex. 97 0.239778513867603 0 0 1 M02A.profile.d50 nuclear ubiquitin ligase complex GO:0000152 A ubiquitin ligase complex found in the nucleus. 30 0.0741583032580215 0 0 1 M02A.profile.d50 protein phosphatase type 2A complex GO:0000159 A heterodimer with protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic and regulatory subunits. 31 0.0766302466999555 0 0 1 M02A.profile.d50 exosome (RNase complex) GO:0000178 Complex of 3'-5' exoribonucleases. 16 0.0395510950709448 0 0 1 M02A.profile.d50 nuclear chromosome GO:0000228 A chromosome found in the nucleus of a eukaryotic cell. 127 0.313936817125624 1 3.18535433070866 0.2697186986707 M02A.profile.d50 cell fraction GO:0000267 A generic term for parts of cells prepared by disruptive biochemical techniques. 1358 3.35689919414644 1 0.297893961708395 0.965301370093488 M02A.profile.d50 integral to membrane of membrane fraction GO:0000299 Integral to that fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes; require detergents, such as Triton X-100, to be released from membranes. 13 0.0321352647451426 0 0 1 M02A.profile.d50 organellar ribosome GO:0000313 A ribosome contained within a subcellular organelle. 43 0.106293568003164 0 0 1 M02A.profile.d50 organellar small ribosomal subunit GO:0000314 The smaller of the two subunits of an organellar ribosome. 14 0.0346072081870767 0 0 1 M02A.profile.d50 organellar large ribosomal subunit GO:0000315 The larger of the two subunits of an organellar ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site). 11 0.0271913778612745 0 0 1 M02A.profile.d50 lytic vacuole GO:0000323 A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. 228 0.563603104760963 0 0 1 M02A.profile.d50 DNA-directed RNA polymerase complex GO:0000428 A protein complex that possesses DNA-directed RNA polymerase activity. 41 0.101349681119296 0 0 1 M02A.profile.d50 proteasome complex (sensu Eukaryota) GO:0000502 A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and the regulatory particle that caps the proteasome core complex. As in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759). 66 0.163148267167647 0 0 1 M02A.profile.d50 chromosome, pericentric region GO:0000775 The central region of a chromosome that includes the centromere and associated proteins. 76 0.187867701586988 0 0 1 M02A.profile.d50 kinetochore GO:0000776 A multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules. 39 0.0964057942354279 0 0 1 M02A.profile.d50 condensed chromosome kinetochore GO:0000777 A multisubunit complex that is located at the pericentric region of a condensed chromosome and provides an attachment point for the spindle microtubules. 7 0.0173036040935383 0 0 1 M02A.profile.d50 condensed chromosome, pericentric region GO:0000779 The central region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. 7 0.0173036040935383 0 0 1 M02A.profile.d50 chromosome, telomeric region GO:0000781 The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins. 34 0.0840460770257577 0 0 1 M02A.profile.d50 chromatin GO:0000785 The ordered and organized complex of DNA and protein that forms the chromosome. 231 0.571018935086765 1 1.75125541125541 0.435449739301391 M02A.profile.d50 nucleosome GO:0000786 A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. 65 0.160676323725713 0 0 1 M02A.profile.d50 nuclear chromatin GO:0000790 The ordered and organized complex of DNA and protein that forms the chromosome in the nucleus. 38 0.0939338507934939 1 10.6457894736842 0.089762880067684 M02A.profile.d50 heterochromatin GO:0000792 A compact and highly condensed form of chromatin. 37 0.0914619073515598 0 0 1 M02A.profile.d50 condensed chromosome GO:0000793 A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure. 77 0.190339645028922 0 0 1 M02A.profile.d50 condensed nuclear chromosome GO:0000794 A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure that remains in the nucleus. 42 0.10382162456123 0 0 1 M02A.profile.d50 synaptonemal complex GO:0000795 A proteinaceous scaffold found between homologous chromosomes during meiosis. 19 0.0469669253967469 0 0 1 M02A.profile.d50 sex chromosome GO:0000803 A chromosome involved in sex determination. 12 0.0296633213032086 0 0 1 M02A.profile.d50 spindle pole GO:0000922 Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules. 35 0.0865180204676917 0 0 1 M02A.profile.d50 gamma-tubulin complex GO:0000930 A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species. 9 0.0222474909774064 0 0 1 M02A.profile.d50 voltage-gated sodium channel complex GO:0001518 A sodium channel in a cell membrane whose opening is governed by the membrane potential. 13 0.0321352647451426 0 0 1 M02A.profile.d50 cornified envelope GO:0001533 An insoluble protein structure formed under the plasma membrane of cornifying epithelial cells. 16 0.0395510950709448 0 0 1 M02A.profile.d50 acrosome GO:0001669 A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome. 15 0.0370791516290107 0 0 1 M02A.profile.d50 stress fiber GO:0001725 Bundle of microfilaments and other proteins found in fibroblasts. 30 0.0741583032580215 0 0 1 M02A.profile.d50 ruffle GO:0001726 Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork. 55 0.135956889306373 0 0 1 M02A.profile.d50 sex chromatin GO:0001739 A condensed mass of compacted chromatin that represents an inactivated X chromosome. 12 0.0296633213032086 0 0 1 M02A.profile.d50 photoreceptor outer segment GO:0001750 The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes. 12 0.0296633213032086 0 0 1 M02A.profile.d50 immunological synapse GO:0001772 An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated lipid rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction. 25 0.0617985860483512 0 0 1 M02A.profile.d50 extracellular region GO:0005576 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. 1426 3.52499134819795 0 0 1 M02A.profile.d50 proteinaceous extracellular matrix GO:0005578 A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. 401 0.991249320215554 0 0 1 M02A.profile.d50 membrane attack complex GO:0005579 A complex produced by sequentially activated components of the complement cascade inserted into a target cell membrane and forming a pore leading to cell lysis via ion and water flow. 7 0.0173036040935383 0 0 1 M02A.profile.d50 collagen GO:0005581 Any of the various assemblies in which collagen chains form a left-handed triple helix; may assemble into higher order structures. 75 0.185395758145054 0 0 1 M02A.profile.d50 fibrillar collagen GO:0005583 Any collagen polymer in which collagen triple helices associate to form fibrils. 28 0.0692144163741534 0 0 1 M02A.profile.d50 collagen type IV GO:0005587 A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form nets within basement membranes. 16 0.0395510950709448 0 0 1 M02A.profile.d50 FACIT collagen GO:0005593 Any collagen polymer associated with collagen fibrils and in which the collagen monomers contain two or more relatively short triple-helical domains connected by non-triple-helical sequences; the acronym FACIT stands for fibril-associated collagen with interrupted triple helix. 7 0.0173036040935383 0 0 1 M02A.profile.d50 basement membrane GO:0005604 A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. 119 0.294161269590152 0 0 1 M02A.profile.d50 basal lamina GO:0005605 A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix. 55 0.135956889306373 0 0 1 M02A.profile.d50 laminin-1 complex GO:0005606 A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha1, beta1 and gamma1. 16 0.0395510950709448 0 0 1 M02A.profile.d50 extracellular space GO:0005615 That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. 647 1.59934740693133 0 0 1 M02A.profile.d50 intracellular GO:0005622 The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. 10805 26.7093488900974 30 1.12320222119389 0.28659617118736 M02A.profile.d50 cell GO:0005623 The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. 14576 36.0310476096307 34 0.943630625686059 0.655113920808655 M02A.profile.d50 membrane fraction GO:0005624 That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes. 1046 2.58565284026301 1 0.386749521988528 0.924893930936754 M02A.profile.d50 soluble fraction GO:0005625 That fraction of cells, prepared by disruptive biochemical methods, that is soluble in water. 333 0.823157166164038 0 0 1 M02A.profile.d50 insoluble fraction GO:0005626 That fraction of cells, prepared by disruptive biochemical methods, that is not soluble in water. 38 0.0939338507934939 0 0 1 M02A.profile.d50 nucleus GO:0005634 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. 5251 12.9801750135957 21 1.61785183774519 0.0245121055598562 M02A.profile.d50 nuclear envelope GO:0005635 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). 229 0.566075048202897 1 1.76655021834061 0.432648283396283 M02A.profile.d50 nuclear inner membrane GO:0005637 The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope. 13 0.0321352647451426 1 31.1184615384615 0.0316629388039029 M02A.profile.d50 nuclear outer membrane GO:0005640 The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes. 8 0.0197755475354724 0 0 1 M02A.profile.d50 nuclear pore GO:0005643 Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. 114 0.281801552380482 0 0 1 M02A.profile.d50 nucleoplasm GO:0005654 That part of the nuclear content other than the chromosomes or the nucleolus. 608 1.5029416126959 2 1.33072368421053 0.443366746274573 M02A.profile.d50 nucleolar ribonuclease P complex GO:0005655 A ribonuclease P complex located in the nucleolus of a eukaryotic cell, where it catalyzes the 5' endonucleolytic cleavage of precursor tRNAs to yield mature tRNAs. Eukaryotic nucleolar ribonuclease P complexes generally contain a single RNA molecule that is necessary but not sufficient for catalysis, and several protein molecules. 6 0.0148316606516043 0 0 1 M02A.profile.d50 replication fork GO:0005657 The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. 42 0.10382162456123 1 9.63190476190476 0.0987297816990099 M02A.profile.d50 DNA replication factor A complex GO:0005662 A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa. 8 0.0197755475354724 0 0 1 M02A.profile.d50 DNA replication factor C complex GO:0005663 A complex of five polypeptides in eukaryotes, and two in prokaryotes, that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. 11 0.0271913778612745 1 36.7763636363636 0.0268577801367799 M02A.profile.d50 DNA-directed RNA polymerase II, core complex GO:0005665 RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template. 30 0.0741583032580215 0 0 1 M02A.profile.d50 DNA-directed RNA polymerase III complex GO:0005666 RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template. 9 0.0222474909774064 0 0 1 M02A.profile.d50 transcription factor complex GO:0005667 Any complex, distinct from RNA polymerase, including one or more polypeptides capable of binding DNA at promoters or at cis-acting regulatory sequences, and regulating transcription. 244 0.603154199831908 1 1.65795081967213 0.453325059657619 M02A.profile.d50 transcription factor TFIID complex GO:0005669 A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters. 22 0.0543827557225491 1 18.3881818181818 0.0529942199196842 M02A.profile.d50 holo TFIIH complex GO:0005675 A complex that contains kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. In S. cerevisiae, it is composed of the 5-subunit core (Rad3, Tfb1, Tfb2, Ssl1, Tfb4), Ssl2p, and TFIIK (Kin28p, Ccl1p, and Tfb3p). All of the subunits have equivalents in humans: the 5 subunit core is composed of XPD, p62, p55, p44, p34; the equivalent of the TFIIK subcomplex is composed of MO15, Mat1, and a cyclin; the human equivalent of Ssl2p is XPB. 5 0.0123597172096702 0 0 1 M02A.profile.d50 chromatin silencing complex GO:0005677 Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing. 11 0.0271913778612745 0 0 1 M02A.profile.d50 chromatin assembly complex GO:0005678 Any protein complex that acts in the formation of nucleosomes or higher order chromatin structure. 13 0.0321352647451426 0 0 1 M02A.profile.d50 anaphase-promoting complex GO:0005680 A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B. 22 0.0543827557225491 0 0 1 M02A.profile.d50 spliceosome GO:0005681 A ribonucleoprotein complex, containing RNA and small nuclear ribonucleoproteins (snRNPs) that is assembled during the splicing of messenger RNA primary transcript to excise an intron. 192 0.474613140851337 0 0 1 M02A.profile.d50 U2-dependent spliceosome GO:0005684 The major (U2-dependent) spliceosome is composed of five snRNP complexes (U1, U2, U4, U5, and U6) as well as many non-snRNP proteins. It acts through many RNA-RNA, RNA-protein, and protein-protein interactions to precisely excise each intron and join the flanking exons. 15 0.0370791516290107 0 0 1 M02A.profile.d50 U12-dependent spliceosome GO:0005689 The minor (U12-dependent) spliceosome is composed of the snRNPs, U11, U12, U4atac, U6atac, and U5 (which is also a component of the major spliceosome). This minor form of the spliceosome is responsible for the splicing of the majority of introns with atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site. 13 0.0321352647451426 0 0 1 M02A.profile.d50 chromosome GO:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. 465 1.14945370049933 2 1.73995698924731 0.319099241625262 M02A.profile.d50 nuclear heterochromatin GO:0005720 A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin. 22 0.0543827557225491 0 0 1 M02A.profile.d50 nucleolus GO:0005730 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. 194 0.479557027735205 1 2.08525773195876 0.381309867448706 M02A.profile.d50 small nucleolar ribonucleoprotein complex GO:0005732 A complex composed of RNA of the small nucleolar RNA (snoRNA) and protein, found in the nucleolus of a eukaryotic cell. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type. 12 0.0296633213032086 0 0 1 M02A.profile.d50 cytoplasm GO:0005737 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 5577 13.7860285756662 10 0.725372063833602 0.880379186345568 M02A.profile.d50 mitochondrion GO:0005739 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. 984 2.4323923468631 2 0.822235772357723 0.698923718658186 M02A.profile.d50 mitochondrial envelope GO:0005740 The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space. 339 0.837988826815642 0 0 1 M02A.profile.d50 mitochondrial outer membrane GO:0005741 The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope. 52 0.128541058980571 0 0 1 M02A.profile.d50 mitochondrial inner membrane GO:0005743 The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae. 253 0.625401690809314 0 0 1 M02A.profile.d50 mitochondrial inner membrane presequence translocase complex GO:0005744 The protein transport machinery of the mitochondrial inner membrane that contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor. 15 0.0370791516290107 0 0 1 M02A.profile.d50 mitochondrial respiratory chain GO:0005746 The protein complexes that form the mitochondrial electron transport system (the respiratory chain). Complexes I, III and IV can transport protons if embedded in an oriented membrane, such as an intact mitochondrial inner membrane. 62 0.153260493399911 0 0 1 M02A.profile.d50 mitochondrial respiratory chain complex I GO:0005747 A part of the respiratory chain located in the mitochondrion. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone. 39 0.0964057942354279 0 0 1 M02A.profile.d50 mitochondrial proton-transporting ATP synthase complex GO:0005753 A proton-transporting ATP synthase complex found in the mitochondrial membrane. 17 0.0420230385128788 0 0 1 M02A.profile.d50 mitochondrial intermembrane space GO:0005758 The region between the inner and outer lipid bilayers of the mitochondrial envelope. 20 0.049438868838681 0 0 1 M02A.profile.d50 mitochondrial matrix GO:0005759 The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty-acid oxidation. 112 0.276857665496613 0 0 1 M02A.profile.d50 mitochondrial ribosome GO:0005761 A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes. 43 0.106293568003164 0 0 1 M02A.profile.d50 mitochondrial large ribosomal subunit GO:0005762 The larger of the two subunits of a mitochondrial ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site). 11 0.0271913778612745 0 0 1 M02A.profile.d50 mitochondrial small ribosomal subunit GO:0005763 The smaller of the two subunits of a mitochondrial ribosome. 14 0.0346072081870767 0 0 1 M02A.profile.d50 lysosome GO:0005764 Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. 228 0.563603104760963 0 0 1 M02A.profile.d50 lysosomal membrane GO:0005765 The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm. 28 0.0692144163741534 0 0 1 M02A.profile.d50 endosome GO:0005768 A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation. 161 0.397982894151382 0 0 1 M02A.profile.d50 early endosome GO:0005769 Small irregularly shaped intracellular vesicles to which endocytosed molecules are initially delivered. 43 0.106293568003164 0 0 1 M02A.profile.d50 late endosome GO:0005770 A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center. 42 0.10382162456123 0 0 1 M02A.profile.d50 vacuole GO:0005773 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. 253 0.625401690809314 0 0 1 M02A.profile.d50 vacuolar membrane GO:0005774 The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell. 32 0.0791021901418896 0 0 1 M02A.profile.d50 autophagic vacuole GO:0005776 A double-membrane bound vesicle in which endogenous cellular material is sequestered; known as autophagosome in yeast. 12 0.0296633213032086 0 0 1 M02A.profile.d50 peroxisome GO:0005777 A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2). 115 0.284273495822416 0 0 1 M02A.profile.d50 peroxisomal membrane GO:0005778 The lipid bilayer surrounding a peroxisome. 34 0.0840460770257577 0 0 1 M02A.profile.d50 integral to peroxisomal membrane GO:0005779 Penetrating at least one phospholipid bilayer of a peroxisomal membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. 18 0.0444949819548129 0 0 1 M02A.profile.d50 endoplasmic reticulum GO:0005783 The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). 922 2.27913185346319 0 0 1 M02A.profile.d50 signal recognition particle, endoplasmic reticulum targeting GO:0005786 A ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. 16 0.0395510950709448 0 0 1 M02A.profile.d50 endoplasmic reticulum lumen GO:0005788 The volume enclosed by the membranes of the endoplasmic reticulum. 29 0.0716863598160874 0 0 1 M02A.profile.d50 endoplasmic reticulum membrane GO:0005789 The lipid bilayer surrounding the endoplasmic reticulum. 159 0.393039007267514 0 0 1 M02A.profile.d50 smooth endoplasmic reticulum GO:0005790 The smooth endoplasmic reticulum (ER) has with no ribosomes attached to it. The smooth is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER. 9 0.0222474909774064 0 0 1 M02A.profile.d50 rough endoplasmic reticulum GO:0005791 The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae. 16 0.0395510950709448 0 0 1 M02A.profile.d50 microsome GO:0005792 Any of the small, heterogeneous, artifactual, vesicular particles, 50-150 nm in diameter, that are formed when some eukaryotic cells are homogenized and that sediment on centrifugation at 100000 g. 217 0.536411726899689 0 0 1 M02A.profile.d50 ER-Golgi intermediate compartment GO:0005793 A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi transport. 55 0.135956889306373 0 0 1 M02A.profile.d50 Golgi apparatus GO:0005794 A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. 514 1.2705789291541 1 0.78704280155642 0.719772056072853 M02A.profile.d50 Golgi stack GO:0005795 The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack. 35 0.0865180204676917 0 0 1 M02A.profile.d50 Golgi-associated vesicle GO:0005798 Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. 88 0.217531022890196 1 4.59704545454545 0.195713981756183 M02A.profile.d50 cis-Golgi network GO:0005801 The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum. 6 0.0148316606516043 0 0 1 M02A.profile.d50 trans-Golgi network GO:0005802 The network of interconnected tubular and cisternal structures located at the side of the Golgi apparatus distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination. 42 0.10382162456123 1 9.63190476190476 0.0987297816990099 M02A.profile.d50 centrosome GO:0005813 A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. 109 0.269441835170811 0 0 1 M02A.profile.d50 centriole GO:0005814 A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle. 14 0.0346072081870767 0 0 1 M02A.profile.d50 microtubule organizing center GO:0005815 A region in a eukaryotic cell, such as a centrosome or basal body, from which microtubules grow. 127 0.313936817125624 0 0 1 M02A.profile.d50 spindle GO:0005819 The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. 92 0.227418796657932 0 0 1 M02A.profile.d50 cytosol GO:0005829 That part of the cytoplasm that does not contain membranous or particulate subcellular components. 687 1.69822514460869 1 0.588850072780204 0.817376307477382 M02A.profile.d50 cytosolic ribosome (sensu Eukaryota) GO:0005830 A ribosome found in the cytosol; this term can also be used to refer to ribosomes associated with the endoplasmic reticulum in eukaryotic cells. As in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759). 127 0.313936817125624 0 0 1 M02A.profile.d50 hemoglobin complex GO:0005833 An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group. 13 0.0321352647451426 0 0 1 M02A.profile.d50 heterotrimeric G-protein complex GO:0005834 Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G-protein coupled receptors to an effector protein. 40 0.098877737677362 0 0 1 M02A.profile.d50 proteasome regulatory particle (sensu Eukaryota) GO:0005838 A multisubunit complex, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex. As in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759). 12 0.0296633213032086 0 0 1 M02A.profile.d50 proteasome core complex (sensu Eukaryota) GO:0005839 A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex. This complex is involved in the proteolysis of substrates in an ATP dependent manner and consists of four ring-like structures, two outer and two inner, each containing seven subunits. As in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759). 27 0.0667424729322193 0 0 1 M02A.profile.d50 ribosome GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. 252 0.62292974736738 0 0 1 M02A.profile.d50 cytosolic large ribosomal subunit (sensu Eukaryota) GO:0005842 The large subunit of a ribosome; has a sedimentation coefficient of 60S. As in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759). 72 0.177979927819252 0 0 1 M02A.profile.d50 cytosolic small ribosomal subunit (sensu Eukaryota) GO:0005843 The small subunit of a eukaryotic cytosolic ribosome; has a sedimentation coefficient of 40S. As in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759). 50 0.123597172096702 0 0 1 M02A.profile.d50 polysome GO:0005844 Several ribosomes bound to one mRNA. 17 0.0420230385128788 1 23.7964705882353 0.0412021928988779 M02A.profile.d50 eukaryotic translation initiation factor 2B complex GO:0005851 A multisubunit guanine nucleotide exchange factor which catalyzes the exchange of GDP bound to initiation factor eIF2 for GTP, generating active eIF2-GTP. In humans, it is composed of five subunits, alpha, beta, delta, gamma and epsilon. 9 0.0222474909774064 1 44.9488888888889 0.0220287769316943 M02A.profile.d50 eukaryotic translation initiation factor 3 complex GO:0005852 A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. 1 0.00247194344193405 0 0 1 M02A.profile.d50 eukaryotic translation elongation factor 1 complex GO:0005853 A multisubunit nucleotide exchange complex that binds GTP and aminoacyl-tRNAs, and catalyzes their codon-dependent placement at the A-site of the ribosome. In humans, the complex is composed of four subunits, alpha, beta, delta and gamma. 6 0.0148316606516043 0 0 1 M02A.profile.d50 cytoskeleton GO:0005856 Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. 1286 3.17891926632719 3 0.943716951788491 0.615986183854527 M02A.profile.d50 axonemal dynein complex GO:0005858 A dynein complex found in eukaryotic cilia and flagella; the motor domain heads interact with adjacent microtubules to generate a sliding force which in converted to a bending motion. May contain two or three dynein heavy chains as well as several light chains. 16 0.0395510950709448 0 0 1 M02A.profile.d50 muscle myosin complex GO:0005859 A filament of myosin found in a muscle cell of any type. 30 0.0741583032580215 0 0 1 M02A.profile.d50 troponin complex GO:0005861 A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction. 6 0.0148316606516043 0 0 1 M02A.profile.d50 striated muscle thick filament GO:0005863 Filaments formed of polymers of a muscle-specific myosin II isoform, found in the middle of sarcomeres in myofibrils. 20 0.049438868838681 0 0 1 M02A.profile.d50 striated muscle thin filament GO:0005865 Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils. 16 0.0395510950709448 0 0 1 M02A.profile.d50 cytoplasmic dynein complex GO:0005868 Any dynein complex that catalyzes movement along a cytoplasmic microtubule; cytoplasmic dynein complexes participates in many transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes,and may include light chains and light intermediate chains. 8 0.0197755475354724 0 0 1 M02A.profile.d50 dynactin complex GO:0005869 A 20S multiprotein assembly of total mass about 1.2 MDa that activates dynein-based activity in vivo. A large structural component of the complex is an actin-like 40 nm filament composed of actin-related protein, to which other components attach. 7 0.0173036040935383 0 0 1 M02A.profile.d50 kinesin complex GO:0005871 Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work. 21 0.051910812280615 0 0 1 M02A.profile.d50 microtubule GO:0005874 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. 260 0.642705294902853 0 0 1 M02A.profile.d50 microtubule associated complex GO:0005875 Any multimeric complex connected to a microtubule. 142 0.351015968754635 0 0 1 M02A.profile.d50 spindle microtubule GO:0005876 Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole. 33 0.0815741335838236 0 0 1 M02A.profile.d50 cytoplasmic microtubule GO:0005881 Any microtubule in the cytoplasm of a cell. 20 0.049438868838681 0 0 1 M02A.profile.d50 intermediate filament GO:0005882 A distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: keratin filaments of mammalian epithelial cells; desmin filaments found in cells of muscles of all types; vimentin filaments found in mesenchymal cells; neurofilaments of neurons; and glial filaments found in all types of glial cells. 93 0.229890740099867 2 8.69978494623656 0.0225292578467665 M02A.profile.d50 neurofilament GO:0005883 A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter. 10 0.0247194344193405 0 0 1 M02A.profile.d50 actin filament GO:0005884 A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. 39 0.0964057942354279 0 0 1 M02A.profile.d50 Arp2/3 protein complex GO:0005885 A stable complex of seven subunits, two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5). Functions in the nucleation of actin filaments. 17 0.0420230385128788 0 0 1 M02A.profile.d50 plasma membrane GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. 2876 7.10930933900232 5 0.703303198887343 0.837083405159261 M02A.profile.d50 integral to plasma membrane GO:0005887 Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. 1846 4.56320759381025 1 0.219144095341278 0.989630193340399 M02A.profile.d50 sodium:potassium-exchanging ATPase complex GO:0005890 Sodium:potassium-exchanging ATPases are tetrameric proteins, consisting of two large alpha subunits and two smaller beta subunits. The alpha subunits bear the active site and penetrate the membrane, while the beta subunits carry oligosaccharide groups and face the cell exterior. 10 0.0247194344193405 0 0 1 M02A.profile.d50 voltage-gated calcium channel complex GO:0005891 A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential. 33 0.0815741335838236 0 0 1 M02A.profile.d50 nicotinic acetylcholine-gated receptor-channel complex GO:0005892 A protein complex that acts as an acetylcholine receptor, and forms a transmembrane channel through which ions may pass in response to ligand binding. The complex is a homo- or heteropentamer of subunits that are members of a neurotransmitter receptor superfamily. 19 0.0469669253967469 0 0 1 M02A.profile.d50 caveola GO:0005901 A small pit, depression, or invagination, such as any of the minute pits or incuppings of the cell membrane formed during pinocytosis, that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Such caveolae may be pinched off to form free vesicles within the cytoplasm. 18 0.0444949819548129 0 0 1 M02A.profile.d50 microvillus GO:0005902 Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. 19 0.0469669253967469 0 0 1 M02A.profile.d50 brush border GO:0005903 Dense covering of microvilli on the apical surface of epithelial cells in the intestine and kidney; the microvilli aid absorption by increasing the surface area of the cell. 20 0.049438868838681 0 0 1 M02A.profile.d50 coated pit GO:0005905 An invagination of the cell membrane of many eukaryotic cells, concerned in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane. During endocytosis it is converted into a coated vesicle. The coat is of clathrin. 93 0.229890740099867 2 8.69978494623656 0.0225292578467665 M02A.profile.d50 intercellular junction GO:0005911 A specialized region of connection between two cells including but not limited to gap junctions, desmosomes, and tight junctions, but excluding direct cytoplasmic junctions such as ring canals. 174 0.430118158896524 1 2.32494252873563 0.349914021669067 M02A.profile.d50 adherens junction GO:0005912 A cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments. 77 0.190339645028922 1 5.25376623376623 0.173516468788228 M02A.profile.d50 cell-cell adherens junction GO:0005913 An adherens junction which connects two cells to each other. 34 0.0840460770257577 1 11.8982352941176 0.0807067650980794 M02A.profile.d50 gap junction GO:0005921 Any specialized areas of the plasma membranes of adjacent cells where the membranes are 2-4 nm apart and penetrated by a connexon. 19 0.0469669253967469 0 0 1 M02A.profile.d50 connexon complex GO:0005922 An assembly of six molecules of connexin, made in the Golgi apparatus and subsequently transported to the plasma membrane, where docking of two connexons on apposed plasma membranes across the extracellular space forms a gap junction. 15 0.0370791516290107 0 0 1 M02A.profile.d50 tight junction GO:0005923 A belt-like region of very close contact between the plasma membranes of adjacent cells so that the intercellular space is completely occluded. They occur in epithelia and brain endothelia. 56 0.138428832748307 0 0 1 M02A.profile.d50 cell-substrate adherens junction GO:0005924 An adherens junction which connects a cell to the extracellular matrix. 41 0.101349681119296 0 0 1 M02A.profile.d50 focal adhesion GO:0005925 Small region on the surface of a cell that anchors the cell to the extracellular matrix and that are points of termination of actin filaments. 37 0.0914619073515598 0 0 1 M02A.profile.d50 cilium GO:0005929 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. 41 0.101349681119296 0 0 1 M02A.profile.d50 axoneme GO:0005930 The bundle of microtubules and associated proteins that forms the core of cilia and flagella in eukaryotic cells and is responsible for their movements. 21 0.051910812280615 0 0 1 M02A.profile.d50 cell cortex GO:0005938 The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. 96 0.237306570425669 0 0 1 M02A.profile.d50 unlocalized protein complex GO:0005941 Used as a holding place for cellular components whose precise localization is, as yet, unknown, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products. 32 0.0791021901418896 0 0 1 M02A.profile.d50 phosphoinositide 3-kinase complex GO:0005942 A complex containing a heterodimer of a catalytic subunit and a regulatory (adaptor) subunit of any phosphoinositide 3-kinase (PI3K). 21 0.051910812280615 0 0 1 M02A.profile.d50 cAMP-dependent protein kinase complex GO:0005952 An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer. 17 0.0420230385128788 0 0 1 M02A.profile.d50 glycine cleavage complex GO:0005960 A multienzyme complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase. 2 0.0049438868838681 0 0 1 M02A.profile.d50 synaptic vesicle GO:0008021 Secretory organelles, some 50 nm in diameter, of presynaptic nerve terminals; accumulate high concentrations of neurotransmitters and secrete these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane. 62 0.153260493399911 0 0 1 M02A.profile.d50 transcription elongation factor complex GO:0008023 Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation. 10 0.0247194344193405 0 0 1 M02A.profile.d50 voltage-gated potassium channel complex GO:0008076 A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential. 89 0.22000296633213 0 0 1 M02A.profile.d50 spectrin GO:0008091 Membrane associated dimeric protein (240 and 220 kDa) of erythrocytes. Forms a complex with ankyrin, actin and probably other components of the membrane cytoskeleton, so that there is a mesh of proteins underlying the plasma membrane, potentially restricting the lateral mobility of integral proteins. 20 0.049438868838681 0 0 1 M02A.profile.d50 signalosome GO:0008180 A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome. 14 0.0346072081870767 0 0 1 M02A.profile.d50 oligosaccharyl transferase complex GO:0008250 A multisubunit protein complex in the endoplasmic reticulum membrane of eukaryotes that transfers lipid-linked oligosaccharide precursor to asparagine residues on nascent proteins; includes at least nine different subunits, at least in yeast. 11 0.0271913778612745 0 0 1 M02A.profile.d50 protein serine/threonine phosphatase complex GO:0008287 A complex, normally consisting of a catalytic and a regulatory subunit, which catalyzes the removal of a phosphate group from a serine or threonine residue of a protein. 54 0.133484945864439 0 0 1 M02A.profile.d50 F-actin capping protein complex GO:0008290 A heterodimer consisting of alpha and a beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments. 12 0.0296633213032086 0 0 1 M02A.profile.d50 integrin complex GO:0008305 Any member of a family of heterodimeric transmembrane receptors for cell-adhesion molecules. The alpha and beta subunits are noncovalently bonded. 52 0.128541058980571 0 0 1 M02A.profile.d50 microtubule-based flagellum GO:0009434 A long, whiplike protrusion from the surface of a eukaryotic cell, whose undulations drive the cell through a liquid medium; similar in structure to a cilium. The flagellum is based on a 9+2 arrangement of microtubules. 11 0.0271913778612745 0 0 1 M02A.profile.d50 external side of plasma membrane GO:0009897 The side of the plasma membrane that is opposite to the side that faces the cytoplasm. 96 0.237306570425669 0 0 1 M02A.profile.d50 basal plasma membrane GO:0009925 Part of the plasma membrane at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis. 18 0.0444949819548129 0 0 1 M02A.profile.d50 cell surface GO:0009986 The external part of the cell wall and/or plasma membrane. 232 0.573490878528699 0 0 1 M02A.profile.d50 endosome membrane GO:0010008 The lipid bilayer surrounding an endosome. 10 0.0247194344193405 0 0 1 M02A.profile.d50 endomembrane system GO:0012505 A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. 657 1.62406684135067 2 1.23147640791476 0.483055406868857 M02A.profile.d50 vesicle membrane GO:0012506 The lipid bilayer surrounding any membrane-bounded vesicle in the cell. 146 0.360903742522371 1 2.77082191780822 0.303265281781765 M02A.profile.d50 ER to Golgi transport vesicle membrane GO:0012507 The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi. 15 0.0370791516290107 0 0 1 M02A.profile.d50 trans-Golgi network transport vesicle membrane GO:0012510 The lipid bilayer surrounding a vesicle transporting substances between the trans-Golgi network and other parts of the cell. 32 0.0791021901418896 1 12.641875 0.0761449755804292 M02A.profile.d50 actin cytoskeleton GO:0015629 The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. 393 0.971473772680081 0 0 1 M02A.profile.d50 microtubule cytoskeleton GO:0015630 The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. 443 1.09507094477678 0 0 1 M02A.profile.d50 large ribosomal subunit GO:0015934 The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). 92 0.227418796657932 0 0 1 M02A.profile.d50 small ribosomal subunit GO:0015935 The smaller of the two subunits of a ribosome. 71 0.175507984377317 0 0 1 M02A.profile.d50 dystrophin-associated glycoprotein complex GO:0016010 A multiprotein complex that forms the critical link between the cytoskeleton and extracellular matrix; typical of, but not confined, to muscle cells. The constituents of the complex are somewhat tissue specific. The rod-like dystrophin forms a link between the actin cytoskeleton and the plasma membrane; links between dystrophin and the extracellular matrix are provided by the sarcoglycan complex. 27 0.0667424729322193 0 0 1 M02A.profile.d50 dystroglycan complex GO:0016011 Includes alpha- and beta-dystroglycan; alternative products of the same gene; the laminin-binding component of the dystrophin-associated glycoprotein complex, providing a link between the subsarcolemmal cytoskeleton (in muscle cells) and the extracellular matrix. Alpha-dystroglycan is an extracellular protein binding to alpha-laminin and to beta-dystroglycan; beta-dystroglycan is a transmembrane protein which binds alpha-dystroglycan and dystrophin. 12 0.0296633213032086 0 0 1 M02A.profile.d50 sarcoglycan complex GO:0016012 Formed of five N-glycosylated sarcoglycans: alpha-, beta-, gamma-, delta-, and epsilon sarcoglycan, single-pass transmembrane proteins that form a complex which is fixed to the dystrophin axis by a lateral association with the dystroglycan complex. 8 0.0197755475354724 0 0 1 M02A.profile.d50 membrane GO:0016020 Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. 6445 15.9316754832649 9 0.564912335143522 0.977301082963321 M02A.profile.d50 integral to membrane GO:0016021 Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. 4626 11.4352103623869 4 0.349796800691742 0.996493365938652 M02A.profile.d50 cytoplasmic membrane-bound vesicle GO:0016023 A membrane-bound vesicle found in the cytoplasm of the cell. 331 0.81821327928017 1 1.2221752265861 0.55922742407992 M02A.profile.d50 prefoldin complex GO:0016272 A multisubunit chaperone that acts to delivers unfolded proteins to cytosolic chaperonin. In humans, the complex is a heterohexamer of two PFD-alpha and four PFD-beta type subunits. 11 0.0271913778612745 0 0 1 M02A.profile.d50 eukaryotic translation initiation factor 4F complex GO:0016281 The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome. 20 0.049438868838681 0 0 1 M02A.profile.d50 eukaryotic 43S preinitiation complex GO:0016282 The 43S preinitiation complex is the 40S ribosomal subunit plus eIF1A, eIF3, and eIF2-GTP-bound to the initiator tRNA. 57 0.140900776190241 1 7.09719298245614 0.131576007610459 M02A.profile.d50 eukaryotic 48S initiation complex GO:0016283 The 48S initiation complex is composed of the 40S ribosomal subunit, the initiator tRNA, and the mRNA. 50 0.123597172096702 0 0 1 M02A.profile.d50 basolateral plasma membrane GO:0016323 Part of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis. 106 0.262026004845009 0 0 1 M02A.profile.d50 apical plasma membrane GO:0016324 Part of the plasma membrane at the apical end of the cell. 47 0.1161813417709 0 0 1 M02A.profile.d50 apicolateral plasma membrane GO:0016327 The apical end of the lateral plasma membrane of epithelial cells. 70 0.173036040935383 0 0 1 M02A.profile.d50 lateral plasma membrane GO:0016328 The membranes on the sides of epithelial cells which lie at the interface of adjacent cells. 15 0.0370791516290107 0 0 1 M02A.profile.d50 nuclear matrix GO:0016363 The dense fibrillar network lying on the inner side of the nuclear membrane. 23 0.0568546991644831 0 0 1 M02A.profile.d50 myosin complex GO:0016459 A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes. 82 0.202699362238592 0 0 1 M02A.profile.d50 myosin II complex GO:0016460 A myosin complex containing two class II myosin heavy chains, two myosin essential light chains and two myosin regulatory light chains. Also known as classical myosin or conventional myosin, the myosin II class includes the major muscle myosin of vertebrate and invertebrate muscle, and is characterized by alpha-helical coiled coil tails that self assemble to form a variety of filament structures. 30 0.0741583032580215 0 0 1 M02A.profile.d50 unconventional myosin complex GO:0016461 A portmanteau term for myosins other than myosin II. 9 0.0222474909774064 0 0 1 M02A.profile.d50 proton-transporting two-sector ATPase complex GO:0016469 A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible. 60 0.148316606516043 0 0 1 M02A.profile.d50 SWI/SNF complex GO:0016514 Any of a family of protein complexes that regulate transcription by remodeling chromatin. Swi/Snf complexes comprise nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components. 17 0.0420230385128788 0 0 1 M02A.profile.d50 sarcoplasm GO:0016528 The cytoplasm of a muscle fiber; includes the sarcoplasmic reticulum. 25 0.0617985860483512 0 0 1 M02A.profile.d50 sarcoplasmic reticulum GO:0016529 A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle fiber; continuous over large portions of the cell and with the nuclear envelope; an endoplasmic reticulum specialized for the sequestration of calcium ions. 21 0.051910812280615 0 0 1 M02A.profile.d50 NuRD complex GO:0016581 An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins. 11 0.0271913778612745 0 0 1 M02A.profile.d50 chromatin remodeling complex GO:0016585 Any complex that mediates dynamic changes in eukaryotic chromatin. 61 0.150788549957977 0 0 1 M02A.profile.d50 DNA-directed RNA polymerase II, holoenzyme GO:0016591 Large protein complex composed of the RNA polymerase core complex and a variety of other proteins including transcription factor complexes TFIIA, D, E, F, and H which are required for promoter recognition, and the Mediator subcomplex. Catalyzes the synthesis of eukaryotic pre-mRNA. 98 0.242250457309537 2 8.25591836734694 0.0248291736441459 M02A.profile.d50 caveolar membrane GO:0016599 The membrane area of caveolae, the small pits, depressions, or invaginations found in the plasma membrane of cells. Caveolar membrane is characterized by the presence of caveolins, which constitute the major protein component of caveolar membrane in vivo. 15 0.0370791516290107 0 0 1 M02A.profile.d50 nuclear body GO:0016604 Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. 86 0.212587136006328 0 0 1 M02A.profile.d50 PML body GO:0016605 A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection. 38 0.0939338507934939 0 0 1 M02A.profile.d50 nuclear speck GO:0016607 A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. 18 0.0444949819548129 0 0 1 M02A.profile.d50 transcriptional repressor complex GO:0017053 A protein complex that possesses activity that prevents or downregulates transcription. 10 0.0247194344193405 0 0 1 M02A.profile.d50 virion GO:0019012 The complete fully infectious extracellular virus particle. 2 0.0049438868838681 0 0 1 M02A.profile.d50 viral capsid GO:0019028 The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres. 2 0.0049438868838681 0 0 1 M02A.profile.d50 synaptosome GO:0019717 Any of the discrete particles (nerve-ending particles) formed from the clublike presynaptic nerve endings that resist disruption and are snapped or torn off their attachments when brain tissue is homogenized in media isosmotic to plasma. 49 0.121125228654768 0 0 1 M02A.profile.d50 flagellum GO:0019861 Long whiplike or feathery structures borne either singly or in groups by the motile cells of many bacteria and unicellular eukaryotes and by the motile male gametes of many eukaryotic organisms, which propel the cell through a liquid medium. 20 0.049438868838681 0 0 1 M02A.profile.d50 organelle inner membrane GO:0019866 The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites. 266 0.657536955554457 1 1.52082706766917 0.482295671670703 M02A.profile.d50 outer membrane GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. 118 0.291689326148218 0 0 1 M02A.profile.d50 extrinsic to plasma membrane GO:0019897 Loosely bound to one surface of the plasma membrane, but not integrated into the hydrophobic region. 50 0.123597172096702 0 0 1 M02A.profile.d50 extrinsic to membrane GO:0019898 Loosely bound to one surface of a membrane, but not integrated into the hydrophobic region. 67 0.165620210609581 0 0 1 M02A.profile.d50 myofibril GO:0030016 The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. 94 0.232362683541801 1 4.3036170212766 0.207569402668961 M02A.profile.d50 sarcomere GO:0030017 The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. 71 0.175507984377317 1 5.69774647887324 0.161151587657948 M02A.profile.d50 Z disc GO:0030018 Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached. 33 0.0815741335838236 1 12.2587878787879 0.078428692949341 M02A.profile.d50 lamellipodium GO:0030027 A thin sheetlike process extended by the leading edge of a crawling fibroblast; contains a dense meshwork of actin filaments. 55 0.135956889306373 1 7.35527272727273 0.127266645466854 M02A.profile.d50 cell junction GO:0030054 A specialized region of connection between two cells or between a cell and the extracellular matrix. 216 0.533939783457755 1 1.87287037037037 0.414096868395268 M02A.profile.d50 cell-matrix junction GO:0030055 A specialized region of connection between a cell and the extracellular matrix. 50 0.123597172096702 0 0 1 M02A.profile.d50 desmosome GO:0030057 Button-like point of intercellular contact through which the intermediate filaments of adjacent cells are connected indirectly. 10 0.0247194344193405 0 0 1 M02A.profile.d50 membrane coat GO:0030117 Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules. 91 0.224946853215998 1 4.4454945054945 0.201663698769778 M02A.profile.d50 clathrin coat GO:0030118 A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes. 60 0.148316606516043 1 6.74233333333333 0.138000186180437 M02A.profile.d50 membrane coat adaptor complex GO:0030119 Any of several heterotetrameric complexes that link clathrin (or another coat-forming molecule, as hypothesized for AP-3 and AP-4) to a membrane surface; they are found on coated pits and coated vesicles, and mediate sorting of cargo proteins into vesicles. 25 0.0617985860483512 1 16.1816 0.0599997083577651 M02A.profile.d50 vesicle coat GO:0030120 A membrane coat found on a coated vesicle. 88 0.217531022890196 1 4.59704545454545 0.195713981756183 M02A.profile.d50 AP-1 adaptor complex GO:0030121 A membrane coat adaptor complex that links clathrin to the membrane surface of a vesicle; vesicles with AP-1-containing coats are normally found primarily in the trans-Golgi network. 8 0.0197755475354724 1 50.5675 0.0196052966743015 M02A.profile.d50 clathrin vesicle coat GO:0030125 A clathrin coat found on a vesicle. 60 0.148316606516043 1 6.74233333333333 0.138000186180437 M02A.profile.d50 COPI vesicle coat GO:0030126 One of two multimeric complexes that forms a membrane vesicle coat. The mammalian COPI subunits are called alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. Vesicles with COPI coats are found associated with Golgi membranes at steady state. 14 0.0346072081870767 0 0 1 M02A.profile.d50 COPII vesicle coat GO:0030127 One of two multimeric complexes that forms a membrane vesicle coat. COPII is best characterized in S. cerevisiae, where the subunits are called Sar1p, Sec13p, Sec31p, Sec23p, and Sec24p. Vesicles with COPII coats are found associated with endoplasmic reticulum (ER) membranes at steady state. 15 0.0370791516290107 0 0 1 M02A.profile.d50 clathrin coat of trans-Golgi network vesicle GO:0030130 A clathrin coat found on a vesicle of the trans-Golgi network. 31 0.0766302466999555 1 13.0496774193548 0.0738555990020986 M02A.profile.d50 clathrin adaptor complex GO:0030131 A membrane coat adaptor complex that links clathrin to a membrane. 21 0.051910812280615 1 19.2638095238095 0.0506474741693736 M02A.profile.d50 clathrin coat of coated pit GO:0030132 The coat found on coated pits and the coated vesicles derived from coated pits; comprises clathrin and the AP-2 adaptor complex. 15 0.0370791516290107 0 0 1 M02A.profile.d50 transport vesicle GO:0030133 Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, and to destinations within or outside the cell. 90 0.222474909774064 1 4.49488888888889 0.199685366259419 M02A.profile.d50 ER to Golgi transport vesicle GO:0030134 A vesicle that mediates transport from the endoplasmic reticulum to the Golgi complex; bears a coat formed of the COPII coat complex proteins; such vesicles found associated with endoplasmic reticulum (ER) membranes at steady state, and are involved in ER to Golgi (anterograde) vesicle transport. 19 0.0469669253967469 0 0 1 M02A.profile.d50 coated vesicle GO:0030135 Small membrane-bounded organelle formed by pinching off of a coated region of membrane. Some coats are made of clathrin, whereas others are made from other proteins. 184 0.454837593315865 1 2.19858695652174 0.36580619673218 M02A.profile.d50 clathrin-coated vesicle GO:0030136 A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes. 144 0.355959855638503 1 2.80930555555556 0.299807889718513 M02A.profile.d50 COPI-coated vesicle GO:0030137 A vesicle with a coat formed of the COPI coat complex proteins. COPI-coated vesicles are found associated with Golgi membranes at steady state, are involved in Golgi to endoplasmic reticulum (retrograde) vesicle transport, and possibly also in intra-Golgi transport. 16 0.0395510950709448 0 0 1 M02A.profile.d50 endocytic vesicle GO:0030139 A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. 43 0.106293568003164 0 0 1 M02A.profile.d50 trans-Golgi network transport vesicle GO:0030140 A vesicle that mediates transport between the trans-Golgi network and other parts of the cell. 43 0.106293568003164 1 9.40790697674418 0.100957670704549 M02A.profile.d50 secretory granule GO:0030141 A small subcellular vesicle, surrounded by a single-layered membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. 50 0.123597172096702 0 0 1 M02A.profile.d50 integral to Golgi membrane GO:0030173 Penetrating at least one phospholipid bilayer of the Golgi complex membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. 48 0.118653285212834 0 0 1 M02A.profile.d50 filopodium GO:0030175 Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone; usually approximately 0.1 um wide, 5-10 um long, can be up to 50 um long in axon growth cones; contains a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward. 16 0.0395510950709448 1 25.28375 0.0388262256909156 M02A.profile.d50 integral to endoplasmic reticulum membrane GO:0030176 Penetrating at least one phospholipid bilayer of an endoplasmic reticulum membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. 55 0.135956889306373 0 0 1 M02A.profile.d50 dynein complex GO:0030286 Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity. 35 0.0865180204676917 0 0 1 M02A.profile.d50 axon GO:0030424 The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter. 66 0.163148267167647 0 0 1 M02A.profile.d50 dendrite GO:0030425 A branching protoplasmic process of a neuron that receive and integrate signals coming from axons of other neurons, and convey the resulting signal to the body of the cell. 54 0.133484945864439 1 7.49148148148148 0.125103951918425 M02A.profile.d50 growth cone GO:0030426 The migrating motile tip of a growing nerve cell axon or dendrite. 31 0.0766302466999555 0 0 1 M02A.profile.d50 site of polarized growth GO:0030427 Any part of a cell where non-isotropic growth takes place. 34 0.0840460770257577 0 0 1 M02A.profile.d50 midbody GO:0030496 A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis. 11 0.0271913778612745 0 0 1 M02A.profile.d50 ribonucleoprotein complex GO:0030529 A macromolecular complex containing both protein and RNA molecules. 574 1.41889553567014 1 0.704773519163763 0.75844356450776 M02A.profile.d50 heterogeneous nuclear ribonucleoprotein complex GO:0030530 Particulate complex of heterogeneous nuclear RNA (hnRNA; a heterogeneous mixture of RNA molecules of high Mr with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, that which is translated into protein) with protein, which is cell-specific and heterogeneous. The protein component may play a role in the processing of the hnRNA to mRNA. 26 0.0642705294902853 0 0 1 M02A.profile.d50 small nuclear ribonucleoprotein complex GO:0030532 A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs. 37 0.0914619073515598 0 0 1 M02A.profile.d50 transport vesicle membrane GO:0030658 The lipid bilayer surrounding a transport vesicle. 47 0.1161813417709 1 8.60723404255319 0.109814290537621 M02A.profile.d50 cytoplasmic vesicle membrane GO:0030659 The lipid bilayer surrounding a cytoplasmic vesicle. 124 0.306520986799822 1 3.26241935483871 0.264276171409276 M02A.profile.d50 Golgi-associated vesicle membrane GO:0030660 The lipid bilayer surrounding a vesicle associated with the Golgi apparatus. 49 0.121125228654768 1 8.25591836734694 0.114209828507162 M02A.profile.d50 coated vesicle membrane GO:0030662 The lipid bilayer surrounding a coated vesicle. 95 0.234834626983735 1 4.25831578947368 0.209528246287221 M02A.profile.d50 COPI coated vesicle membrane GO:0030663 The lipid bilayer surrounding a COPI-coated vesicle. 14 0.0346072081870767 0 0 1 M02A.profile.d50 clathrin coated vesicle membrane GO:0030665 The lipid bilayer surrounding a clathrin-coated vesicle. 61 0.150788549957977 1 6.63180327868852 0.140131000967157 M02A.profile.d50 endocytic vesicle membrane GO:0030666 The lipid bilayer surrounding an endocytic vesicle. 16 0.0395510950709448 0 0 1 M02A.profile.d50 secretory granule membrane GO:0030667 The lipid bilayer surrounding a secretory granule. 24 0.0593266426064172 0 0 1 M02A.profile.d50 synaptic vesicle membrane GO:0030672 The lipid bilayer surrounding a synaptic vesicle. 19 0.0469669253967469 0 0 1 M02A.profile.d50 ribonuclease P complex GO:0030677 A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs. 7 0.0173036040935383 0 0 1 M02A.profile.d50 multimeric ribonuclease P complex GO:0030681 A ribonuclease P complex that generally contains a single RNA molecule and several protein molecules. 6 0.0148316606516043 0 0 1 M02A.profile.d50 cortical cytoskeleton GO:0030863 The portion of the cytoskeleton that lies just beneath the plasma membrane. 41 0.101349681119296 0 0 1 M02A.profile.d50 cortical actin cytoskeleton GO:0030864 The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane. 31 0.0766302466999555 0 0 1 M02A.profile.d50 RNA polymerase complex GO:0030880 Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits. 42 0.10382162456123 0 0 1 M02A.profile.d50 replisome GO:0030894 A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins. 13 0.0321352647451426 0 0 1 M02A.profile.d50 anchoring collagen GO:0030934 Any collagen polymer which links one collagen assembly, such as a collagen fibril or sheet, to other structures. 18 0.0444949819548129 0 0 1 M02A.profile.d50 sheet-forming collagen GO:0030935 Any collagen polymer in which collagen triple helices associate to form sheet-like networks. 18 0.0444949819548129 0 0 1 M02A.profile.d50 NADH dehydrogenase complex (quinone) GO:0030964 Complex that possesses NADH dehydrogenase (quinone) activity. 39 0.0964057942354279 0 0 1 M02A.profile.d50 extracellular matrix GO:0031012 A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as in plants). 406 1.00360903742522 0 0 1 M02A.profile.d50 organelle membrane GO:0031090 The lipid bilayer surrounding an organelle. 934 2.3087951747664 2 0.866252676659529 0.671540495360265 M02A.profile.d50 intrinsic to membrane GO:0031224 Located in a membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane. 4637 11.4624017402482 4 0.34896700452879 0.996565410077381 M02A.profile.d50 anchored to membrane GO:0031225 Tethered to a membrane by a covalently attached anchor, such as a lipid moiety, that is embedded in the membrane. When used to describe a protein, indicates that none of the peptide sequence is embedded in the membrane. 7 0.0173036040935383 0 0 1 M02A.profile.d50 intrinsic to plasma membrane GO:0031226 Located in the plasma membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane. 1855 4.58545508478766 1 0.218080862533693 0.989858627498128 M02A.profile.d50 intrinsic to endoplasmic reticulum membrane GO:0031227 Located in the endoplasmic reticulum membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane. 58 0.143372719632175 0 0 1 M02A.profile.d50 intrinsic to Golgi membrane GO:0031228 Located in the Golgi membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane. 56 0.138428832748307 0 0 1 M02A.profile.d50 intrinsic to peroxisomal membrane GO:0031231 Located in the peroxisomal membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane. 18 0.0444949819548129 0 0 1 M02A.profile.d50 leading edge GO:0031252 The area of a motile cell closest to the direction of movement. 105 0.259554061403075 1 3.8527619047619 0.228852329425735 M02A.profile.d50 intrinsic to organelle membrane GO:0031300 Located in an organelle membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane. 150 0.370791516290107 0 0 1 M02A.profile.d50 integral to organelle membrane GO:0031301 Penetrating at least one phospholipid bilayer of an organelle membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. 136 0.336184308103031 0 0 1 M02A.profile.d50 cytoplasmic vesicle GO:0031410 A vesicle formed of membrane or protein, found in the cytoplasm of a cell. 344 0.850348544025313 1 1.17598837209302 0.573183579177716 M02A.profile.d50 nonmotile primary cilium GO:0031513 An immotile primary cilium that may be missing the central pair of microtubules, or the central pair of microtubules and outer dynein arms. Some primary cilia also have altered arrangements of outer microtubules (fewer than nine and/or not always present as doublets). Nonmotile primary cilia typically function as sensory organelles that concentrate and organize sensory signaling molecules. 14 0.0346072081870767 0 0 1 M02A.profile.d50 PcG protein complex GO:0031519 A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure. 18 0.0444949819548129 0 0 1 M02A.profile.d50 neuromuscular junction GO:0031594 The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a post-synaptic potential responsible of the muscle contraction. 13 0.0321352647451426 0 0 1 M02A.profile.d50 A band GO:0031672 The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line. 20 0.049438868838681 0 0 1 M02A.profile.d50 microbody membrane GO:0031903 The lipid bilayer surrounding a microbody. 34 0.0840460770257577 0 0 1 M02A.profile.d50 filamentous actin GO:0031941 A two-stranded helical polymer of the protein actin. 11 0.0271913778612745 0 0 1 M02A.profile.d50 nuclear membrane GO:0031965 Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. 147 0.363375685964305 1 2.75197278911565 0.304987570599232 M02A.profile.d50 mitochondrial membrane GO:0031966 Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. 308 0.761358580115687 0 0 1 M02A.profile.d50 organelle envelope GO:0031967 A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. 560 1.38428832748307 1 0.722392857142857 0.7499269224199 M02A.profile.d50 organelle outer membrane GO:0031968 The outer, i.e. cytoplasm-facing, lipid bilayer of an organelle envelope. 60 0.148316606516043 0 0 1 M02A.profile.d50 organelle envelope lumen GO:0031970 The region between the inner and outer lipid bilayers of an organelle envelope. 27 0.0667424729322193 0 0 1 M02A.profile.d50 membrane-enclosed lumen GO:0031974 The enclosed volume within a sealed membrane or between two sealed membranes. 945 2.33598655262768 3 1.28425396825397 0.413590785747739 M02A.profile.d50 envelope GO:0031975 A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer, also includes the space between layers. 562 1.38923221436694 1 0.719822064056939 0.751161727355521 M02A.profile.d50 mitochondrial lumen GO:0031980 The volume enclosed by the mitochondrial inner membrane. 112 0.276857665496613 0 0 1 M02A.profile.d50 nuclear lumen GO:0031981 The volume enclosed by the nuclear inner membrane. 771 1.90586839373115 3 1.57408560311284 0.297832562217203 M02A.profile.d50 vesicle GO:0031982 Any small, fluid-filled, spherical organelle enclosed by membrane or protein. 357 0.882483808770455 1 1.13316526610644 0.586697841390713 M02A.profile.d50 organelle subcompartment GO:0031984 A membrane-enclosed compartment that is a part of an organelle. 15 0.0370791516290107 0 0 1 M02A.profile.d50 Golgi cisterna GO:0031985 Any of the thin, flattened membrane-bounded compartments that form the central portion of the Golgi complex. 13 0.0321352647451426 0 0 1 M02A.profile.d50 membrane-bound vesicle GO:0031988 Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer. 343 0.847876600583379 1 1.17941690962099 0.572125898598784 M02A.profile.d50 integrator complex GO:0032039 A protein complex that stably associates with the C-terminus of RNA polymerase II and mediates 3'-end processing of small nuclear RNAs generated by RNA polymerase II. 13 0.0321352647451426 0 0 1 M02A.profile.d50 cell division site GO:0032153 The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. The cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane. The mitotic, or meiotic, spindle is aligned perpendicular to the division plane. 7 0.0173036040935383 0 0 1 M02A.profile.d50 cell division site part GO:0032155 Any constituent part of the cell division plane, the eventual plane of cell division in a dividing cell. 7 0.0173036040935383 0 0 1 M02A.profile.d50 actin filament bundle GO:0032432 An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. 30 0.0741583032580215 0 0 1 M02A.profile.d50 myosin filament GO:0032982 A protein complex containing myosin heavy chains, plus associated light chains and other proteins, in which the myosin heavy chains are arranged into a filament. 20 0.049438868838681 0 0 1 M02A.profile.d50 macromolecular complex GO:0032991 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. 2816 6.96099273248628 5 0.718288352272727 0.82375984807842 M02A.profile.d50 proton-transporting two-sector ATPase complex, proton-transporting domain GO:0033177 A protein complex that forms part of a proton-transporting two-sector ATPase complex and carries out proton transport across a membrane. The proton-transporting domain (F0, V0, or A0) includes integral and peripheral membrane proteins. 17 0.0420230385128788 0 0 1 M02A.profile.d50 proton-transporting two-sector ATPase complex, catalytic domain GO:0033178 A protein complex that forms part of a proton-transporting two-sector ATPase complex and catalyzes ATP hydrolysis or synthesis. The catalytic domain (F1, V1, or A1) comprises a hexameric catalytic core and a central stalk, and is peripherally associated with the membrane when the two-sector ATPase is assembled. 13 0.0321352647451426 0 0 1 M02A.profile.d50 ribosomal subunit GO:0033279 Either of the two ribonucleoprotein complexes that associate to form a ribosome. 161 0.397982894151382 0 0 1 M02A.profile.d50 histone methyltransferase complex GO:0035097 A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins. 9 0.0222474909774064 0 0 1 M02A.profile.d50 ciliary rootlet GO:0035253 A cytoskeleton-like structure, originating from the basal body at the proximal end of a cilium, and extending proximally toward the cell nucleus. Rootlets are typically 80-100 nm in diameter and contain cross striae distributed at regular intervals of approximately 55-70 nm. 13 0.0321352647451426 0 0 1 M02A.profile.d50 NuA4 histone acetyltransferase complex GO:0035267 A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60). 13 0.0321352647451426 0 0 1 M02A.profile.d50 T cell receptor complex GO:0042101 A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. 14 0.0346072081870767 0 0 1 M02A.profile.d50 nuclear envelope-endoplasmic reticulum network GO:0042175 The continuous network of membranes encompassing the outer nuclear membrane and the endoplasmic reticulum. 170 0.420230385128788 0 0 1 M02A.profile.d50 sarcolemma GO:0042383 The outer membrane of a muscle fiber, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers. 9 0.0222474909774064 0 0 1 M02A.profile.d50 melanosome GO:0042470 A tissue-specific, membrane bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells. 17 0.0420230385128788 0 0 1 M02A.profile.d50 microbody GO:0042579 Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2). 115 0.284273495822416 0 0 1 M02A.profile.d50 zymogen granule GO:0042588 A membrane-bound, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme. 15 0.0370791516290107 0 0 1 M02A.profile.d50 vesicular fraction GO:0042598 Any of the small, heterogeneous, artifactual, vesicular particles that are formed when some cells are homogenized. 222 0.548771444109359 0 0 1 M02A.profile.d50 MHC protein complex GO:0042611 A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. 84 0.20764324912246 0 0 1 M02A.profile.d50 MHC class I protein complex GO:0042612 A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules. 58 0.143372719632175 0 0 1 M02A.profile.d50 MHC class II protein complex GO:0042613 A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. 26 0.0642705294902853 0 0 1 M02A.profile.d50 chylomicron GO:0042627 A particle composed of a central core of triglycerides surrounded by a protein-phospholipid coating. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues. 12 0.0296633213032086 0 0 1 M02A.profile.d50 mitochondrial intermembrane space protein transporter complex GO:0042719 Soluble complex of the mitochondrial intermembrane space composed of various combinations of small Tim proteins; acts as a protein transporter to guide proteins to the Tim22 complex for insertion into the mitochondrial inner membrane. 7 0.0173036040935383 0 0 1 M02A.profile.d50 presynaptic membrane GO:0042734 A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane. 12 0.0296633213032086 0 0 1 M02A.profile.d50 GPI-anchor transamidase complex GO:0042765 An enzyme complex which in humans and yeast consists of at least five proteins; for example, the complex contains GAA1, GPI8, PIG-S, PIG-U, and PIG-T in human, and Gaa1p, Gab1p, Gpi8p, Gpi16p, and Gpi17p in yeast. Catalyzes the posttranslational attachment of the carboxyl-terminus of a precursor protein to a GPI-anchor. 6 0.0148316606516043 0 0 1 M02A.profile.d50 cell projection GO:0042995 A prolongation or process extending from a cell, e.g. a flagellum or axon. 323 0.798437731744698 1 1.25244582043344 0.550413140314926 M02A.profile.d50 neuron projection GO:0043005 A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. 127 0.313936817125624 1 3.18535433070866 0.2697186986707 M02A.profile.d50 cell soma GO:0043025 The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. 51 0.126069115538636 0 0 1 M02A.profile.d50 H4/H2A histone acetyltransferase complex GO:0043189 A multisubunit complex that catalyzes the acetylation of histones H4 and H2A. 14 0.0346072081870767 0 0 1 M02A.profile.d50 ATP-binding cassette (ABC) transporter complex GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. 16 0.0395510950709448 0 0 1 M02A.profile.d50 dendritic spine GO:0043197 Protrusion from a dendrite. Spines are specialised subcellular compartments involved in the synaptic transmission. They are linked to the dendritic shaft by a restriction. Because of their bulb shape, they function as a biochemical and an electrical compartment. Spine remodeling is though to be involved in synaptic plasticity. 13 0.0321352647451426 0 0 1 M02A.profile.d50 fibril GO:0043205 Extracellular matrix material consisting of polysaccharides and protein. 12 0.0296633213032086 0 0 1 M02A.profile.d50 organelle GO:0043226 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. 8844 21.8618678004647 23 1.05206015377657 0.431907565829978 M02A.profile.d50 membrane-bound organelle GO:0043227 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. 7809 19.303406338063 23 1.19149955179921 0.227627567033867 M02A.profile.d50 non-membrane-bound organelle GO:0043228 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. 2107 5.20838483215504 6 1.15198860939725 0.42059729872226 M02A.profile.d50 intracellular organelle GO:0043229 Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. 8838 21.8470361398131 23 1.05277438334465 0.430649885446537 M02A.profile.d50 intracellular membrane-bound organelle GO:0043231 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. 7804 19.2910466208533 23 1.19226294208098 0.22675301782809 M02A.profile.d50 intracellular non-membrane-bound organelle GO:0043232 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. 2107 5.20838483215504 6 1.15198860939725 0.42059729872226 M02A.profile.d50 organelle lumen GO:0043233 The volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear membrane lumen. 945 2.33598655262768 3 1.28425396825397 0.413590785747739 M02A.profile.d50 protein complex GO:0043234 Any protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups. 2341 5.78681959756761 5 0.86403246475865 0.685713196182486 M02A.profile.d50 receptor complex GO:0043235 Any protein group composed of two or more subunits, which may or may not be identical, which undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. 118 0.291689326148218 0 0 1 M02A.profile.d50 laminin complex GO:0043256 A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes. 19 0.0469669253967469 0 0 1 M02A.profile.d50 contractile fiber GO:0043292 Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. 106 0.262026004845009 1 3.81641509433962 0.230758562852774 M02A.profile.d50 apical junction complex GO:0043296 A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in invertebrates is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability. 70 0.173036040935383 0 0 1 M02A.profile.d50 nuclear replication fork GO:0043596 The Y-shaped region of a nuclear replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. 16 0.0395510950709448 0 0 1 M02A.profile.d50 nuclear replisome GO:0043601 A multi-component enzymatic machine at the nuclear replication fork, which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins. 13 0.0321352647451426 0 0 1 M02A.profile.d50 extracellular matrix part GO:0044420 Any constituent part of the extracellular matrix, the structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as often seen in plants). 187 0.462253423641667 0 0 1 M02A.profile.d50 extracellular region part GO:0044421 Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite. 983 2.42992040342117 0 0 1 M02A.profile.d50 organelle part GO:0044422 Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. 3305 8.16977307559203 8 0.979219364599092 0.57067296928218 M02A.profile.d50 virion part GO:0044423 Any constituent part of a virion, a complete fully infectious extracellular virus particle. 2 0.0049438868838681 0 0 1 M02A.profile.d50 intracellular part GO:0044424 Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. 10196 25.2039353339596 26 1.03158493526873 0.463311667227168 M02A.profile.d50 membrane part GO:0044425 Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. 5232 12.9332080881989 8 0.618562691131498 0.944275743631237 M02A.profile.d50 chromosomal part GO:0044427 Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. 389 0.961585998912345 2 2.0798971722365 0.250095258586541 M02A.profile.d50 nuclear part GO:0044428 Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. 1318 3.25802145646908 5 1.53467374810319 0.229627717827031 M02A.profile.d50 mitochondrial part GO:0044429 Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. 435 1.07529539724131 0 0 1 M02A.profile.d50 cytoskeletal part GO:0044430 Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. 720 1.77979927819252 2 1.12372222222222 0.531415397999648 M02A.profile.d50 Golgi apparatus part GO:0044431 Any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. 268 0.662480842438325 1 1.5094776119403 0.484851979874686 M02A.profile.d50 endoplasmic reticulum part GO:0044432 Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. 182 0.449893706431997 0 0 1 M02A.profile.d50 cytoplasmic vesicle part GO:0044433 Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell. 132 0.326296534335294 1 3.06469696969697 0.27870025533915 M02A.profile.d50 vacuolar part GO:0044437 Any constituent part of a vacuole, a closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. 36 0.0889899639096258 0 0 1 M02A.profile.d50 microbody part GO:0044438 Any constituent part of a microbody, a cytoplasmic organelle, spherical or oval in shape, that is bounded by a single membrane and contains oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2). 36 0.0889899639096258 0 0 1 M02A.profile.d50 peroxisomal part GO:0044439 Any constituent part of a peroxisome, a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2). 36 0.0889899639096258 0 0 1 M02A.profile.d50 endosomal part GO:0044440 Any constituent part of an endosome, a membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation. 10 0.0247194344193405 0 0 1 M02A.profile.d50 cilium part GO:0044441 Any constituent part of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. 17 0.0420230385128788 0 0 1 M02A.profile.d50 cytoplasmic part GO:0044444 Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 3772 9.32417066297523 6 0.643488865323436 0.902904437671841 M02A.profile.d50 cytosolic part GO:0044445 Any constituent part of cytosol, that part of the cytoplasm that does not contain membranous or particulate subcellular components. 206 0.509220349038414 0 0 1 M02A.profile.d50 intracellular organelle part GO:0044446 A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. 3292 8.13763781084689 8 0.983086269744836 0.566273753888526 M02A.profile.d50 axoneme part GO:0044447 Any constituent part of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia and flagella in eukaryotic cells and is responsible for their movements. 17 0.0420230385128788 0 0 1 M02A.profile.d50 cell cortex part GO:0044448 Any constituent part of the cell cortex, the region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. 57 0.140900776190241 0 0 1 M02A.profile.d50 contractile fiber part GO:0044449 Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. 92 0.227418796657932 1 4.39717391304348 0.203637140954062 M02A.profile.d50 microtubule organizing center part GO:0044450 Any constituent part of a microtubule organizing center, a region in a eukaryotic cell, such as a centrosome or basal body, from which microtubules grow. 35 0.0865180204676917 0 0 1 M02A.profile.d50 nucleoplasm part GO:0044451 Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus. 489 1.20878034310575 2 1.65456032719836 0.340637033865283 M02A.profile.d50 nucleolar part GO:0044452 Any constituent part of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. 31 0.0766302466999555 0 0 1 M02A.profile.d50 nuclear membrane part GO:0044453 Any constituent part of the nuclear membrane, the envelope that surrounds the nucleus of eukaryotic cells. 133 0.328768477777228 1 3.04165413533835 0.280483267512633 M02A.profile.d50 nuclear chromosome part GO:0044454 Any constituent part of a nuclear chromosome, a chromosome found in the nucleus of a eukaryotic cell. 86 0.212587136006328 1 4.70395348837209 0.191722890135011 M02A.profile.d50 mitochondrial membrane part GO:0044455 Any constituent part of the mitochondrial membrane, either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. 112 0.276857665496613 0 0 1 M02A.profile.d50 synapse part GO:0044456 The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. 117 0.289217382706284 0 0 1 M02A.profile.d50 plasma membrane part GO:0044459 Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. 2374 5.86839373115143 4 0.681617523167649 0.836998119269441 M02A.profile.d50 cell projection part GO:0044463 Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon. 56 0.138428832748307 0 0 1 M02A.profile.d50 cell part GO:0044464 Any constituent part of a cell, the basic structural and functional unit of all organisms. 14575 36.0285756661888 34 0.943695368782161 0.654963589117874 M02A.profile.d50 keratin filament GO:0045095 A filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells. The keratins are the most diverse classes of IF proteins, with a large number of keratin isoforms being expressed. Each type of epithelium always expresses a characteristic combination of type I and type II keratins. 5 0.0123597172096702 0 0 1 M02A.profile.d50 intermediate filament cytoskeleton GO:0045111 Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell. 93 0.229890740099867 2 8.69978494623656 0.0225292578467665 M02A.profile.d50 pronucleus GO:0045120 The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents. 10 0.0247194344193405 0 0 1 M02A.profile.d50 lipid raft GO:0045121 Specialized membrane domains composed mainly of cholesterol and sphingolipids, and relatively poor in polyunsaturated lipids such as glycerophospholipids. The formation of these membrane domains is promoted by the presence of cholesterol in the lipid bilayer: the rigid hexagonal rings of cholesterol can pack tightly against the saturated hydrocarbon chains of some membrane lipids, allowing these lipids to assemble into cohesive units floating in the mass of loosely packed polyunsaturated plasma membrane components. 46 0.113709398328966 0 0 1 M02A.profile.d50 apical part of cell GO:0045177 The apical region of a cell. 79 0.19528353191279 0 0 1 M02A.profile.d50 basal part of cell GO:0045178 The basal region of a cell. 20 0.049438868838681 0 0 1 M02A.profile.d50 synapse GO:0045202 The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. 242 0.59821031294804 0 0 1 M02A.profile.d50 postsynaptic membrane GO:0045211 A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters across the synaptic cleft and transmit the signal to the postsynaptic membrane. 102 0.252138231077273 0 0 1 M02A.profile.d50 tricarboxylic acid cycle enzyme complex GO:0045239 Any of the heteromeric enzymes that act in the TCA cycle. 11 0.0271913778612745 0 0 1 M02A.profile.d50 proton-transporting ATP synthase complex GO:0045259 A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient. 29 0.0716863598160874 0 0 1 M02A.profile.d50 proton-transporting ATP synthase complex, catalytic core F(1) GO:0045261 The sector of a hydrogen-transporting ATP synthase complex in which the catalytic activity resides; it comprises the catalytic core and central stalk, and is peripherally associated with a membrane, such as the plasma membrane or the mitochondrial inner membrane, when the entire ATP synthase is assembled. 12 0.0296633213032086 0 0 1 M02A.profile.d50 proton-transporting ATP synthase complex, coupling factor F(o) GO:0045263 All non-F1 subunits of a hydrogen-transporting ATP synthase, including integral and peripheral membrane proteins. 17 0.0420230385128788 0 0 1 M02A.profile.d50 respiratory chain complex I GO:0045271 Respiratory chain complex I is an enzyme of the respiratory chain. It consists of at least 34 polypeptide chains and is L-shaped, with a horizontal arm lying in the membrane and a vertical arm that projects into the matrix. The electrons of NADH enter the chain at this complex. 39 0.0964057942354279 0 0 1 M02A.profile.d50 clathrin-coated endocytic vesicle GO:0045334 A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. 20 0.049438868838681 0 0 1 M02A.profile.d50 anchored to plasma membrane GO:0046658 Tethered to the plasma membrane by a covalently attached anchor, such as a lipid moiety, that is embedded in the membrane. When used to describe a protein, indicates that the peptide sequence does not span the membrane. 7 0.0173036040935383 0 0 1 M02A.profile.d50 pore complex GO:0046930 Any small opening in a membrane that allows the passage of gases and/or liquids. 127 0.313936817125624 0 0 1 M02A.profile.d50 perinuclear region of cytoplasm GO:0048471 Cytoplasm situated near, or occurring around, the nucleus. 87 0.215059079448262 0 0 1 M02A.profile.d50 coated membrane GO:0048475 A single or double lipid bilayer with any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes. 91 0.224946853215998 1 4.4454945054945 0.201663698769778 M02A.profile.d50 signal recognition particle GO:0048500 A complex of protein and RNA which facilitates translocation of proteins across membranes. 16 0.0395510950709448 0 0 1 M02A.profile.d50 pigment granule GO:0048770 A small, subcellular membrane-bound vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. 17 0.0420230385128788 0 0 1 M02A.profile.d50 nuclear DNA-directed RNA polymerase complex GO:0055029 A protein complex, located in the nucleus, that possesses DNA-directed RNA polymerase activity. 41 0.101349681119296 0 0 1 M02A.profile.d50 neurofilament cytoskeleton GO:0060053 Intermediate filament cytoskeletal structure that is made up of neurofilaments. Neurofilaments are specialized intermediate filaments found in neurons. 10 0.0247194344193405 0 0 1 M02A.profile.d50