Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set of expressed genes follow but also to disclose the relationships between these genes. With availability of more genomics, transcriptomics and proteomics data, interactions between genes involve in multiple pathways become more clear and also relationships between the genes, their transcripts, and their gene products. However, existing tools and dbs mainly based on knowledge driven approach in which pathways will be identified by finding the correlation between the information in one of the pathway knowledge databases (KEGG,Reactome,Panther,BioCarta, Panther,GO,NCI,WikiPathways,etc) and gene expression result for a specific conditions for instance tumor, obesity , cold resistant crops/plants, etc.
Introductory Articles/ppt/sources:
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
http://davetang.org/muse/tag/pathway/
https://www.biostars.org/p/42219/
http://bioinformatics.ca//files/public/Pathways_2014_Module4_v2.pdf
http://bioinformatics.ca//files/public/Pathways_2014_Module2.pdf
Impotant Database and Tools:
GeneMANIA, Cytoscape, IPA and Metacore (Commerical ), Pathway Commons, Reactome ,Panther, BioCyc, WikiPathways, Pathvisio, KEGG, NCI, Stringdb, Amigo, WebGestalt ,ConsensusPathDB ,GSEA,Blast2go
Popular R based tools:
Reactome.db, ReactomePA, ClusterProfiler, Gage, SPIA, topGO, Pathview,DOSE,GOStat
More:
http://www.bioconductor.org/help/search/index.html?q=Enrichment+analysis+
Comments
The Database for Annotation, Visualization and Integrated Discovery (DAVID ) are able to visualize genes on BioCarta & KEGG pathway maps. Other options for pathway-mining such as gene functional classification, functional annotation chart or clustering and functional annotation table are also available in DAVID.
http://david.abcc.ncifcrf.gov/
http://www.nature.com/nprot/journal/v4/n1/abs/nprot.2008.211.html
Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
Paper:
http://bioinformatics.oxfordjournals.org/content/29/14/1830.full