extracting a gene from a gmt file

Question

[Bogdan]

Dear all,

Starting from a conversation at : https://bioinformatics.stackexchange.com/questions/5400/how-to-convert-data-in-gmt-format-to-dataframe, would you please advise:

Given a gmt file, how could extract the pathways that are associated with a specific gene?

Thank you very much!

Bogdan

[cpad0112]

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[Ram]

Please use sensible tags that highlight the subject matter of your post. The current tags are nonsensical and show no effort.

Answer 1

[Sam]

Considering the format of the gmt file, I guess the easiest way will be to do

grep -f <file with gene> -w <gmt file>