Wikiomics:Pathway analysis

After determining a list of genes involved in a given biological process the next step is to map these genes to known pathways/Gene Ontology terms and determine i.e. which pathways are overrepresented in a given set of genes.

Recent review: Nam, Dougu, and Seon-Young Kim. “Gene-set approach for expression pattern analysis.” Brief Bioinform (17, 2008): bbn001. HTML

Recommended

• g:Profiler a web-based toolset for functional profiling of gene lists from large-scale experiments. Easy to use web server

• KOBAS server used for i.e. elucidating pathways in addicion

Li, Chuan-Yun, Xizeng Mao, and Liping Wei. “Genes and (Common) Pathways Underlying Drug Addiction.” PLoS Computational Biology 4, no. 1 (1, 2008) HTML

• GSEA http://www.broad.mit.edu/gsea/software/software_index.html

objections (Damian D, Gorfine M. Statistical concerns about the GSEA procedure): http://www.nature.com/ng/journal/v36/n7/full/ng0704-663a.html and reply: http://www.nature.com/ng/journal/v36/n7/full/ng0704-663b.html

Other tools to check

• GEPAT Genome Expression Pathway Analysis Tool. Performs standard microarray analyzes plus "Ensembl database and provides information about gene names, chromosomal location, GO categories and enzymatic activity for each probe on the chip.". Complex installation of java jars/MySQL etc.
• ErmineJ Java stand-alone program "designed to be used by biologists with little or no informatics background" + command line for expert
• PAGE Parametric Analysis of Gene Set Enrichment
• CPath database and software suite for storing, visualizing, and analyzing biological pathways demo page
• EASE (old?) http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=14519205

• nonparametric multivariate analysis Nettleton et al. HTML. R code availebla from author.

Pathway Databases

• KEGG first choice for scope
• Reactome human + model organisms pathways. Expert annotations from literature.
• PID Pathway Interaction Database @NIH

• BioCyc
• Cyclone - provides an open source Java API for easier access to BioCyc.
• RegulonDB E.coli K12 DB (operons/genes/regulatory elements)