Supplemental Tables
If all you would just like is to access the supplemental
tables (in HTML) then click on corresponding link under “Supplemental Tables”.
If you are interested in obtaining the supplemental tables
in an easy to download format, i.e., tab-delimited text files, then click on
the corresponding link under “Supplemental Tables – Download”.
Full Group Profiles Results
The full results for all of the group profiles is available
through this website. This brief tutorial will walk you through an example
analysis process. Specifically, we will follow the example presented in the
corresponding manuscript that found the interesting results for the
Antipsychotic group profile.
First, we need to go to the results overview page for the
“CMAP ATC Level 3 Groups”
The following image depicts the overview slide. The first
column contains the ATC group profile. Hovering the mouse over the ATC code
will show the full group name and clicking on the link directs the user to the
complete ATC code listing on World Health Organization (WHO) Collaborating
Centre for Drug Statistics Methodology website. The “Profile” column contains a
link to a tab-delimited representation of the group profile that was created
and the “Similar” column links to the results obtained when querying the
database with this signature (also tab-delimited). The rest of the columns
contain the web formatted results from the L2L analysis. This analysis is
broken down into the types of lists used to evaluate the signatures against,
i.e., the three GO lists (Biological Processes, Molecular Function, and
Cellular Components), miRNA, Modules, Reactome, and a custom L2L list that is
aggregated from published lists of DEGs. For each of these lists, the
up-expressed (U), down-expressed (D) and up- and down-expressed together, or
both (B), are analyzed. Once again, hovering over any of the links will give
some of this organizational information as the list is long and we recognize
that it is difficult to keep track of the columns.
Antipsychotic (N05A) example:
The first thing is to find the antipsychotic profile
information in the list of results. The ATC classification code for
antipsychotic agents is N05A:
We can click on the first “U” to see the L2L analysis that
corresponds to the GO Biological Process list. On this list we see the most
significantly over-represented GO Biological Processes. As discussed in the
corresponding manuscript, the most over-represented GO Biological Process is
Sterol Biosynthetic Process. For a complete description from AmiGO of any of
the GO terms you can click on the name in the first column. For each list, the
total number of probes mapped to any genes on the gene expression chip that was
used is listed, e.g., 49 for the Sterol Biosynthetic Process list. The number
of expected matches at random would be 0.12 and the actual number of matches is
shown as 13. To find out more information about these 13 probes you can click
on the number. Lastly, the fold enrichment and corresponding p-value are shown
in the table as well.
Example detailed exploration of matches:
