Question: identification of single pathway from microarray data
gravatar for rohit
4.0 years ago by
rohit30 wrote:

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?




R microarray softwares pathways • 1.2k views
ADD COMMENTlink modified 4.0 years ago by Chris Evelo10.0k • written 4.0 years ago by rohit30

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

Go through them.

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

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Deepak Tanwar4.0k
gravatar for TriS
4.0 years ago by
United States, Buffalo
TriS3.9k wrote:

funny, this is similar to a question I replied by mistake earlier: A: 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

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.

ADD COMMENTlink written 4.0 years ago by TriS3.9k
gravatar for Chris Evelo
4.0 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

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.

ADD COMMENTlink written 4.0 years ago by Chris Evelo10.0k
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