Pathway Analysis papers anyone?

Question

[Behram Radmanesh]

My main objective it to get an overview regarding the current state for pathway analysis. To this end I have been trying to find good (recent) papers that talk about different pathway analysis tools/databases.

I have read the follow paper: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375

It was very good and has given me a basic idea for the state of the field up until 2012.
Now when I say 'pathway analysis' I mean, taking a list of genes and linking them to a pathway using a public database. The linking process can be done using database tools or a separate tool the looks at information from various databases, e.g. KEGG or GO.

Could someone please provide me links to a few additional papers or give me an informal overview of where the field is as of 2012.

Thank you!

Note: My understanding of this topic is almost entirely based on the information contained within the paper mentioned above.

Answer 1

[Charles Warden]

Here is a preprint that, according to Twitter speculation, might have caused DAVID to be updated after a 6 year hiatus in new annotations:

http://biorxiv.org/content/early/2016/04/19/049288

Preprints in action. DAVID is updated soon after @reimand preprint showing how stale it is https://t.co/0abev4xJqU https://t.co/fPoOxulgxC

— Anthony Gitter (@anthonygitter) May 26, 2016

[EagleEye]

Awesome preprint article.

Answer 2

[st.ph.n]

You can do a google scholar search for 'pathway analysis', and on the left hand side of the results, click 'Since 2012'.

[Behram Radmanesh]

I have used Google Scholar extensively, in fact I found the paper above and also this one that I am just about the read: http://www.sciencedirect.com/science/article/pii/S0168952512000364

But once again even this paper is from 2012. At the moment I am getting the feeling that there just hasn't been a good review paper on pathway analysis since 2012.

[frcamacho]

Updated: http://nar.oxfordjournals.org/content/44/W1/W205.long http://www.sciencedirect.com/science/article/pii/S1672022914001065 http://journal.frontiersin.org/article/10.3389/fphys.2013.00278/full

[Behram Radmanesh]

Did you read my original question...?

Answer 3

[ablanchetcohen]

This is the first paper that a quick Google search returned.

Pathway-based Analysis Tools for Complex Diseases: A Review http://www.sciencedirect.com/science/article/pii/S1672022914001065

It's just a description of the pathway analysis tools available though.

I'm interested in the subject since I'm trying to find an up-to-date open source software to do pathway analysis, and I find that the development of these tools is lagging. The databases are not always up-to-date, comprehensive enough, or ambitious enough in their objectives, so it's not surprising that it's hard to find a good review of these tools. My Google searches always end up pointing me to Ingenuity Pathway Analysis. I do know about DAVID, Panther, Reactome, Cytoscape, ...

Answer 4

[EagleEye]

GeneSCF is real-time based tool uses current database from KEGG, REACTOME and Gene Ontology.

Gene Set Clustering based on Functional annotation (GeneSCF)

I have compared available tools with GeneSCF performance.The article is under major revision.

[GenoMax]

I am curious as to how are you able to provide current content from KEGG when it requires a subscription for access?

[EagleEye]

GeneSCF uses rest API (Only Gene level) for retrieving information from KEGG,

http://www.genome.jp/kegg/rest/keggapi.html

[ablanchetcohen]

Why do none of these open source programs attempt to do like IPA and integrate the fold changes or the p-values into the pathway analysis?

[russhh]

what, unlike GSEA?

[ablanchetcohen]

GSEA does integrate the fold-changes and the p-values, but it is more of an enrichment analysis then an actual pathway analysis like IPA. You don't get an actual pathway from GSEA.