SigTerms: a bioinformatics tool for
linking gene expression profiling results with gene class associations
Chad Creighton, Ph.D.
Baylor College of Medicine
creighto@bcm.edu
Description
The
SigTerms software tool is a set of Excel macros for use in linking functional
gene class associations to a given set of genes. For each gene class, SigTerms tests whether
the class appears a disproportionate number of times within the given gene
set. Significantly enriched gene classes
may represent significant features that underlie the set of genes as a whole. Given a set of genes of interest, SigTerms
will do the following:
- Find all classes that apply to
each of the genes, the classes being defined by any number of ways,
including Gene Ontology (GO) annotation, predicted microRNA targeting, and
oncogenic pathways.
- Count the number of occurrences
for each class in the gene set of interest.
- For each class, calculate the
probability of finding the same number of occurrences or more of the class
in a randomly selected set of genes of the same number as the set of
interest.
- Tabulate the results in Excel
spreadsheets.
Reference
Creighton
CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH.
A bioinformatics tool for linking gene expression profiling results with public
databases of microRNA target predictions.
RNA. Epub 2008 Sep 23. PMID: 18812437
Documentation
- Instructions
for use
- Tutorial
with examples on using the FindSignificantTerms macro
- Additional
notes on searching for microRNA targeting associations
- For novice Excel users, a tutorial on some useful Excel features
- Tables mapping mirBase accession
numbers to common microRNA names
- Table mapping mirBase
human accession numbers to mouse accession numbers
Excel
workbook with SigTerms macros
- SigTerms.xls –
available from the SourceForge Downloads page
Annotation
files
- Gene Ontology (GO) annotation terms (updated 01/29/09)
- microRNA gene targeting
predictions
- miRanda (www.microRNA.org)
- TargetScan (v 5.0)
- PicTar
- Oncogenic gene signatures
- Molecular
Signature Database (MSigDB, v2)