Determining the transcription factor activators for a particular gene
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4 months ago
Thoth • 0

I'm wondering if there is a way using the existing bioinformatic databases to determine the set of transcriptional activators for a particular gene.

For instance, suppose I was trying to do gene knockout by using a precision-nuclease such as Cas9 to delete the transcription factors which are known to promote/activate transcription for that gene.

I can determine the likely locations of particular transcription factor binding sites in silico using motif detection, or ex vivo using ChIP-seq, but I would need to correlate this information with gene expression / transcription activity data to determine which transcription factors are most responsibility for gene activity. Is there a database(s) for this, or a way to programmatically obtain this information?

I am aware of these two Biostars threads,

List of known transcription factor binding sites along with the type of transcription factors (activator/repressor) in hg19 genome

Transcriptional repressors and transcriptional activators

but the responses are unsatisfactory.

regulation tfbs transcription • 366 views
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If you have single-cell RNA-seq data this might come in handy: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937676/

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