identification of single pathway from microarray data

Question

[rohit]

Hi everyone,

I have analysed affymetrix microarray. After normalizing and removing duplicate entrez id's I'm left with approximately 17,000 genes.

I want to know that out of these 17,000 genes which genes lies in a particular pathway which is of my interest and how to get each gene's involvement in that pathway.

Is there trial or free software or R program which can help me to achieve this?

[Deepak Tanwar]

On the right side of your post, there is Similar posts

Go through them.

There are number of software tools, Bioconductor packages to do this analysis. Depends on the question you are trying to answer.

Answer 1

[TriS]

Funny, this is similar to a question I replied by mistake earlier: Transcriptional repressors and transcriptional activators

In this case tho you can grep the name of the pathway, i.e.,

cat gene_association.goa_human | grep -i "NamePathwayGoesHERE"

and it will return the genes in that GO term

The same applies for the part on MSigDB, you can download the ones you are interested in an parse them as lists in R to find the one you are interested in.

Answer 2

[Chris Evelo]

This is the inverse of this question: How To Find The Pathways In Which A Given Gene Or Protein Is Involved?

You are looking for genes in a pathway while there the question was to find pathways for a gene. Since most tools that can do one of these things also can do the other you might want to check that question.