Question regarding CAGE and UCSC promoters and enhancers
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7 weeks ago
peter ▴ 10

I have download a promoter bed file from UCSC. And I have a promoter bed file from CAGE. In case of UCSC I look 1000bases upstream from gene and download that as bed file. I want to do the union of two bed files but before I do I need to look 1000bases upstream too in CAGE bed file too?

Furthermore, I was looking into enhancers database and for each enhancer position they've mentioned start, and end but also centre position. Why is it important to report the centre position for enhancers?

Insights will be appreciated.

bed CAGE promoter UCSC • 257 views
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7 weeks ago
Charles Plessy ★ 2.8k

The CAGE peaks that you downloaded are peaks of transcription start activity and can be very narrow. If you are looking for transcription factor binding sites, then you need to search in windows of upstream sequences like you did for the UCSC gene starts.

By the way, if you need a more curated set of CAGE peaks, have a look at the FANTOM CAT.

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Thank you @charles-plessy. Just one more question. Should I look 2000 bases upstream or 1000 bases is fine?

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These are quite arbitrary thresholds, and in mammalian genomes some regulators can bind at a much further distance. I do not have recent experience on the topic but I think I remember that 1000 base pairs is fine. A couple years a go we were routinely using [-500,+300] windows for instance (because some regulators can bind downstream...).

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