Human Gene Regulatory Database

Question

[pavishivakumar]

Is there a database that houses human gene-gene (regulatory/transcriptional) interactions that are experimentally validated? Kind of like HPRD or BioGrid is for protein interactions, but for gene regulatory interactions instead? And, if so, is it available freely for public use?

Answer 1

[Obi Griffith]

This is the stated purpose of such resources as ORegAnno and Pazar. Both are efforts to collect and curate experimentally proven transcription factor binding sites (linking at regulator TF to its target TFBS and associated gene wherever possible). However, there are many more related databases and datasets (e.g., ChIP-seq) available through the Encode project and others that might be of use to you.

Update: You might also check out these related posts:

• How to identify targets of a Transcription factor?
• target promoters of a transcription factor
• Determine whether a gene product is a Transcription Factor
• TF and gene(s) regulated by them
• Determine transcription factors for genes

[pavishivakumar]

Awesome Thanks!

Answer 2

[pengchy]

another integrated database: RegNetwork

http://www.regnetworkweb.org/

Answer 3

[majidgeek]

There is a manually curated database of human and mouse transcriptional regulatory networks named TRRUST

Answer 4

[Sasha Fokin]

ONCO.IO is an integrated knowledge database and network analysis tool for exploring complex gene regulatory networks. Database content is based on the manually curated annotation of experimentally verified molecular interactions described in the literature and includes microRNAs, lncRNAs, mRNAs, signaling proteins and transcription factors interactions.

Answer 5

[c.chakraborty]

You can also view the regulatory tract of the genomic region you're interested at the UCSC genome browser. Scroll down to "Expression and Regulation", and by selecting different datasets (based on the study you're interested in) you can assess the location of promoters, TFBS motifs and methylation/acetylation sites.