Question

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

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4.8 years ago

jon.klonowski ▴ 150

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

IPA RNA-Seq NGS dataanalysis • 3.4k views

ADD COMMENT • link updated 4.8 years ago by Morris_Chair ▴ 350 • written 4.8 years ago by jon.klonowski ▴ 150

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has it ever been?

ADD REPLY • link 4.8 years ago by Martombo ★ 3.1k

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

ADD REPLY • link 4.8 years ago by Kevin Blighe 87k

score 1 · Answer 1 · 2019-07-08

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4.8 years ago

Arup Ghosh 3.2k

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

ADD COMMENT • link 4.8 years ago by Arup Ghosh 3.2k

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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.

ADD REPLY • link 4.8 years ago by Kevin Blighe 87k

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

ADD REPLY • link 4.8 years ago by Arup Ghosh 3.2k

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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.

ADD REPLY • link 4.8 years ago by GenoMax 141k

score 1 · Answer 2 · 2019-07-10

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/

score 1 · Answer 3 · 2019-07-10

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4.8 years ago

Morris_Chair ▴ 350

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

ADD COMMENT • link 4.8 years ago by Morris_Chair ▴ 350

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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).

ADD REPLY • link 4.8 years ago by GenoMax 141k

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

ADD REPLY • link 4.8 years ago by Morris_Chair ▴ 350