How to merge metabolic or regulatory pathways from a list of genes

Question

[friasoler]

Hello everybody

I have list of genes that change among conditions and the probability associated to their log2foldchange...I would like to see the pathways that are related with these genes and ...in any way highlight the genes with probability p<0,05 for example....The list of ontology term I can manage but Id like to have like a chart with all the enzymes and metabolites of the pathways and for example in different colors the genes I could detect and the ones that really change......Ill appreciate your help

Roberto

Answer 1

[Parham]

I used pathway visualization of this workflow and was very useful: http://www.bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

[dago]

This is a really nice package!Thanks for sharing. It also uses pathview to map the resutls to KEGG

[Parham]

You're welcome. However if you found it useful you could give the post a thumbs up or something =)

Answer 2

[dago]

You could take a look at pathview (R/Bioconductor). 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.