What’s the answer? Genes–>Pathway

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Question of the week:

Mapping genes to pathway


I have a set of gene identifiers(RefSeq) and I want to know the pathways in which these genes are present along with some statistical score.

Any suggestions for tools.

Thank you


This is a question we see pretty frequently, and there are a number of tools that can help. The selected answer includes both tool suggestions and some useful references. But other answers also flesh out the options. Have a look at the answers, and add others if you have favorites methods for doing this.

Update–I’ll just note that one of the answers comes from Chris Evelo, and I just saw this tweet about him:

RT @larry_parnell: Nice! Congratulations! @Chris_Evelo just received an Agilent Thought Leader Award to Bridge Pathways, Metabolic Models and Gene Annotations

Congrats to Chris! Check out what a “thought leader” has to say on this topic over at BioStar.