Benchmarking TFBS in yeast

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9.7 years ago

by0 ▴ 110

Hi,

I am constructing my own position weight matrices (PWMs) and scoring regions of the yeast genome, for a list of predicted TFBS. I am then using different features to filter this list, in effort to minimize the false positive rate.

My question is, since there is no experimentally defined functional tfbs in yeast (at least that I know of), what is the best way to benchmark my features?

Thank you!

expression benchmark transcription pwm tfbs • 1.8k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by by0 ▴ 110

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What do you mean there are no experimentally verified tfbs in yeast? There are whole databases of them if you google a bit.

ADD REPLY • link 9.7 years ago by Devon Ryan 104k

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Let me clarify, I meant functional tfbs. My filtering is in effort to identify functional tfbs. I will update the question

ADD REPLY • link 9.7 years ago by by0 ▴ 110

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If there really aren't any (I find that difficult to believe, but I suppose it could happen), then why not just validate the sites for at least one transcription factor? There's at least one published method for this using a one-hybrid approach. Then you'd have the known positives you need.

ADD REPLY • link 9.7 years ago by Devon Ryan 104k

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None that are annotated and readily accessible from a database in the public domain for yeast. Thanks for the tip though.

ADD REPLY • link 9.7 years ago by by0 ▴ 110

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