SigTerms tutorial: using the “FindSignificantTerms” macro

1. SigTerms tutorial: using the “FindSignificantTerms” macro Chad Creighton, Ph.D.

2. Selecting the Annotation workbook • The SigTerms web site provides links to download pre-compiled Annotation workbooks for several types of gene class associations of potential interest (e.g. GO terms, microRNA targeting predictions). • Annotation workbook should be specific to the gene array that was used for the profiling. • All genes in the workbook should be represented on the array (any genes not on the array should not be represented in the Annotation workbook) • Workbooks specific to particular array platforms are available for download • User can construct his or her own Annotation workbook and specify gene-to-term associations • Details on Annotation workbook format on web site.

3. Open both SigTerms.xls and Annotation workbook in Excel • Make sure your Excel allows the running of macros (see web site for details).

4. In the Annotation workbook, insert a new worksheet • (Right-click on the worksheet tab, select “Insert”, and choose “New Worksheet.)

5. In the new worksheet, paste the list of selected genes in the first column (starting from the first row). • Use Entrez gene number to specify gene • Duplicate Ids are okay. • For statistical calculations, should not include NULL or “---” or “///” containing entries, only entries for genes with Entrez numbers.

6. Run the “FindSignificantTerms” macro. • Selected gene worksheet should be “active” (i.e. at the front of all the other sheets) when running the macro. • Alt+F8 or Tools->Macros (32-bit Excel) displays the SigTerms macros.

7. Specify the gene population • If choose “number of entries in Annotation sheet”, then selected gene list should not have any entries not in the Annotation worksheet • Otherwise, specify the number of unique, identified genes on the array (for pre-compiled Annotation workbooks, “Gene Pop” sheet has this number).

8. “Enriched Terms” output worksheet lists gene class terms ranked by statistical enrichment • “Terms with Genes” output worksheet lists, for each term, the genes that fall under that term.

9. If desired, one can link additional information to the genes (or microRNAs) listed in the output worksheets. • Can use “MATCH” and “INDEX” Excel functions (Illustrated above and in our Excel tutorial).