Finding transcriptional regulators of a gene
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4.5 years ago
Pappu ★ 1.9k

I am trying to find out transactional regulators, transcription factor binding sites, epigenetic modifications, enhancers, miRNA binding etc. of a gene say TP53 highly expressed in cancer. I am wondering if there is any good resource for that.

RNA-Seq ChIP-Seq • 4.2k views
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4.5 years ago
Denise CS ★ 5.1k

Have you tried Ensembl? You could get the TFBS and histone markers and the annotation of promoters and enhancers from the Ensembl Regulatory Build. Ensembl also has Other Regulatory Data including miRNA targets from Diana TarBase. Check the gene page of TP53 for an example on how to view this on the browser. There are other ways to access the data (programmatically for example).

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4.5 years ago
ZhouK.R. ▴ 10

ChIPBase ( http://rna.sysu.edu.cn/chipbase ) is aimed to explore the transcriptional features of genes by integrating a large amount of ChIP-seq data.In their websever, the "Regulator" module can help you retrieve transcriptional regulators (transcription factors, transcription co-factors and histone modifications) that bound at upstream or downstream of the TSS of your interested gene.

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