Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data?

Question

[jon.klonowski]

Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data? Are there better alternatives out there?

[Martombo]

has it ever been?

[Kevin Blighe]

Better than other commercial products. I have no relationship to Qiagen, for the record.

Answer 1

[Arup Ghosh]

IPA is used for pathway analysis, there is some other premium software available like GeneGo MetaCore, Advaitabio pathway analysis.

[Kevin Blighe]

I agree. People are still very much using it (I am not, though). It is one of those bioinformatics commercial products that appears to be surviving quite nicely alongside the open source packages. People publish results using it, too.

[Arup Ghosh]

They are still in the market because of some of the group leaders thinks a particular pathway term can get their articles published.

[GenoMax]

If you subject area is well covered by IPA then it can literally save you months of PubMed work. It is also a general resource for building hypotheses using interactions encoded in their database, even if you don't have any data of your own.

Answer 2

[Charles Warden]

While you can't guarantee that IPA will work for any given project, I think it is often useful. However, I think having access to open-source alternatives is very important (sometimes as a replacement for some projects, sometimes as a complement to extend understanding for other projects).

I think the website is currently encountering some issues during an upgrade, but I would usually recommend Enrichr:

https://amp.pharm.mssm.edu/Enrichr/

You may also find GATHER results to be useful:

https://changlab.uth.tmc.edu/gather/

Answer 3

[Morris_Chair]

I'm not a fun of this tools but I guess a similar (free) alternative is this:

https://advaitabio.com/ipathwayguide/

you can find a well explained tutorial on youtube

[GenoMax]

While you can create a free account (and possibly do some limited analysis) this software is not free. See FAQ for additional details (Do you offer a free trial section).

[Morris_Chair]

Oh pardon, I used for a short time in the past and I thought was free, thank you genome