Transcript Tutorial - SigTerms

SigTerms tutorial: using the
“FindSignificantTerms” macro
Chad Creighton, Ph.D.
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.
• Open both SigTerms.xls and Annotation workbook
in Excel
• Make sure your Excel allows the running of macros
(see web site for details).
• In the Annotation workbook, insert a new worksheet
• (Right-click on the worksheet tab, select “Insert”,
and choose “New Worksheet.)
• 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.
• 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.
• 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).
• “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.
• 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).