Practical Comparison Of Features Offered By Pathway Analysis Software: Ipa Vs Metacore

Question

[indranipoddar]

Hello All,

Can you please ( if available) provide any detail comparison of pathway analyses between IPA and Metacore, I have found some text from web about their features but couldn't find a practical comparison from somebody who has used both. Whether these software pathway analyses are good for cancer or autoimmune gene sets etc.

Thanks in advance, Indrani

[jpleasance]

Hi

Metacore has disease ontologies and annotation. A direct comparison of databases can be found at: http://www.ncbi.nlm.nih.gov/pubmed/21356087. Your analysis is best with a better quality database.

[Shicheng Guo]

Yes. What about KEGG and Reactome.

Answer 1

[Woa]

Such feature wise comparisons probably do not exist, however there are much heterogeneity between databases, so far as interactions or edges are concerned. Check this reference for the extent of edge heterogeneity among databases like GeneGO, Reactome, String, NCI etc. http://www.biomedcentral.com/1752-0509/6/29 http://www.biomedcentral.com/1752-0509/6/29/figure/F4

and you may find this forum post helpful http://www.sharedproteomics.com/forum/showthread.php?402-Ingenuity-Pathway-Analysis%28IPA%29-vs.-GeneGO-Metacore

[indranipoddar]

Thank you for your answer. Indrani