Pathway Analysis is usually performed with aim to enrich the genes with its functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particulat gene follow but also to diclose relationships between the genes. With availability of more genomics, transcriptomics and proteomics, interactions between genes involve in multiple pathwaya become more clear. However existing tools more based on knowledge driven approach in which pathways identified by finding the correlation between information in one of the pathway knowledge databases (KEGG,Reactome,Panther,BioCarta, Panther,GO,NCI,WikiPathways,etc) with gene expression result for a specific conditions for instance tumor, obesity and cold resistant crops/plants.
Introductory Article/ppt:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375
http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/Pathway%20Analysis.pdf
http://gettinggeneticsdone.blogspot.de/2012/03/pathway-analysis-for-high-throughput.html
https://www.biostars.org/p/42219/
Impotant Database and Tools:
GeneMANIA, Cytoscape,IPA, Pathway Commons, Reactome,Panther, BioCyc, WikiPathways, Pathvisio, KEGG, NCI, Stringdb, WebGestalt ,ConsensusPathDB ,GSEA,Blast2go
Popular R based tools:
Reactome.db, ReactomePA, ClusterProfiler, Gage, SPIA, topGO, Pathview,DOSE
More:
http://www.bioconductor.org/help/search/index.html?q=Enrichment+analysis+
