Ingenuity Pathway Analysis(IPA) vs. GeneGO Metacore

[woa]

How many of you use Ingenuity Pathway Analysis(IPA) or GeneGO Metacore for pathway analysis in quantitative proteomics? What are their relative merits and demerits? How open source software/databases compare against these two commercial tools?

Thanks in advance

[karthikuttan]

I have used IPA. The feature that makes IPA different from all other tools is that they have a very good and widely-accepted knowledge base. IPA is, as you all know, the most popular tool not only because it helps in analyzing the data at multiple levels but also because it provides beautiful representations/figures of pathways/networks. With regard to proteomcs, it is nice to have a look at this article.

I have not used Metacore, so I do not wish to comment on this. I have also used DAVID and PANTHER which are open-source tools mainly dealing with functional annotation/classification. DAVID performed well as far as my specific goals of the experiments were concerned.

And, I should say that there is no Ultimate Tool/Software for any kind of analysis.

[woa]

Thanks !! Here's another relevant paper:

Pathway analysis software: Annotation errors and solutions

http://www.ncbi.nlm.nih.gov/pubmed/20663702

[stugendreich]

Hi all,

I am Product Management director for IPA. I wanted to let you know that there are many hundreds of publications using IPA for proteomics analysis specifically. You can see them here: http://bit.ly/wk1AoJ.

Let me know if you have questions about IPA.

Stuart Tugendreich, PhD

[woa]

Hello Stuart,

Is it possible to use IPA with any 3rd Party opensource software like R/Bioconductor and Cytoscape?

[Infinity]

Is it possible to analyze yeast data in IPA or is it only for mammalian cells?

[stugendreich]

Hello Stuart,

Is it possible to use IPA with any 3rd Party opensource software like R/Bioconductor and Cytoscape?

You can use R, Bioconductor or other packages upstream to generate datasets to load into IPA. We don't (at this time) generally offer the ability to use such tools "inside" of IPA. You can send gene lists to GeneSpring from within IPA. And you can import Cytoscape pathways into IPA.

Can you elaborate on what you are trying to do with those other tools? I'd be interested to hear.

[stugendreich]

IPA is geared towards analysis of mammalian genes and proteins.

[Virginie]

I found that IPA is extremely helpful for analysis for quantitative analysis of proteomics analysis with one caveat: It is very much biased towards cancer. For this reason, I found that the analysis of canonical pathways is sometimes better done using other search engines that in my case are more immunology based and then load the results into KEGG.