Question: What is Pathway Analysis?
2
gravatar for Pranavathiyani G
3.0 years ago by
Pondicherry, India
Pranavathiyani G220 wrote:

How can one define pathway analysis and what are the tools or databases available for pathway analysis? What can be inferred from the result of this analysis? Can I go for pathway analysis if I have only a list of gene symbols(Eg: ATM, CTGF, EGR1, IGF1, etc)?

ADD COMMENTlink written 3.0 years ago by Pranavathiyani G220
1

I would recommend you first google "Pathway Analysis," in order to obtain a better understanding.

Yes, you can use pathway analysis on a list of gene symbols.

ENRICHR seems to be the hot new tools everyone is using these days

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by informatics bot560
1

LMGTFY is not an answer that a potential user expect from BioStars. Given that there are more than one tool to do pathway analyses, a link to Enrichr is indeed a right answer. Often these kind of relevant suggestions won't come in a google search.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Khader Shameer18k
1

Thats true. But there is no evidence from the question that the user has tried to find the answer first and got confused about which tool to use out of many. But as you pointed out, its may not be the best way to welcome a new user.

ADD REPLYlink written 3.0 years ago by geek_y9.4k
1

So the important question here is What biological question you are trying to address? Where does this list of genes came from?. Of course you can do pathway analysis with a list of gene symbols. See what answers google is giving with the same question, What is pathway analysis?. And look at the first hit of another search How to do pathway analysis with a list of genes?

ADD REPLYlink written 3.0 years ago by venu6.1k
1

LMGTFY is not a right way to welcome a new user. BioStar is an expert forum, and the user is looking for "expert opinion" instead of browsing and manually gathering knowledge from a google search.

ADD REPLYlink written 3.0 years ago by Khader Shameer18k
1

Hello Pranavathiyani G!

We believe that this post does not fit the main topic of this site.

This looks like an assignment and you could have searched google first, As Lando mentioned, you could explore ENRICHR to look for pathways enriched for your gene list.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.0 years ago by geek_y9.4k
2

This post is indeed a very relevant topic of the site. Please go easy on newbies - few useful suggestions would be helpful to get them started.

ADD REPLYlink written 3.0 years ago by Khader Shameer18k
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