Supplemental Tables

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:


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