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