Which tool for CRM enrichment?

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2.8 years ago

Filago ▴ 100

Hello guys,

I am interested in conducting CRM (cis-regulatory module) enrichment analysis in selected sequences. Screening the literature, I figured out, that a lot of tools in that field were published in the early 2000s and are not available anymore (rly. frustrating to click on all that "links to nowhere" :) ). On the other hand, the still available tools tend to be Web-server solutions, what makes custom preferences more complicated/impossible.

Maybe someone knows a CRM enrichment tool fulfilling the following points:

Local installation (so no web-server)
Custom sequences and custom TFBS allowed
Capability to deal with a large number of TFBS

Many thanks in advance!

Andreas

CRM TFBS • 753 views

ADD COMMENT • link 2.7 years ago by Filago ▴ 100

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What is "CRM enrichment analysis"?

ADD REPLY • link 2.8 years ago by ATpoint 87k

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Hello, a CRM enrichment analysis is an enrichment analysis of TFBS-pairs (but can also be TFBS-trios, TFBS-quartets...) in e.g. promoters of a certain gene set compared to a background geneset.

Best, Andreas

ADD REPLY • link 2.7 years ago by Filago ▴ 100

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