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Modify all instances of interactions between a particular transcription factor and all target promoters?

asked 2018-05-22 15:14:30 -0500

gpharhay gravatar image


I've got a particular transcription factor and target binding sites associated with a promoter identified throughout the genome. Is it possible to change the regulatory interaction, for all binding sites, from "Unknown" to "Repressor", in one fell swoop instead of marching through the TF's regulon and changing each interaction, one-by-one, using the Regulatory Interaction Editor? Lisp code would work just fine if necessary. Thanks.

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answered 2018-05-23 00:38:40 -0500

Suzanne Paley gravatar image

updated 2018-05-23 00:40:14 -0500

Sure, it's easy using the Lisp API:

(loop for regframe in (get-slot-values 'TF 'regulates)
      do (put-slot-value regframe 'mode "-"))

Substitute the frame id of your transcription factor for TF.

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Thanks, Suzanne!

gpharhay gravatar imagegpharhay ( 2018-05-24 11:26:49 -0500 )edit

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Asked: 2018-05-22 15:14:30 -0500

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Last updated: May 23 '18