Pathways / SAFE

Description

Searches for over- or under-represented genes for KEGG categories.

Parameters

• Phenodata column to test (...)
• Minimum category size (1...100) [10]
• P value threshold (0-1) [0.05]
• Image width (200...3200) [600]
• Image height (200...3200) [600]

Details

This tool takes a filtered gene list, and uses information about the genes, their expression and grouping (from the phenodata group-column) to estimate the over-representation of the gene in the categories. As such, this method is very similar to GSEA analysis from the Broad Institute.

Output

Output is an text file with a list of significant categories, and a safe plot for the most significant category.

References

If you use this tool, please cite:

Barry,W.T., Nobel, A.B. and Wright, F.A. (2005): Significance Analysis of functional categories in gene expression studies: a structured permutation approach, Bioinformatics, 21(9):1943-1949.