Gene Regulatory Database

Question

[Tom A]

Hello,

I am trying to find a database that contains a list of experimentally validated homo sapiens gene regulatory relationships, both TF-gene or gene-gene (transcriptional and/or post-translational) based.

I know of TRANSFAC and JASPAR but I cannot seem to find a comprehensive two-column downloadable (.txt, .csv, etc) file that contains the relationships, perhaps in this format:

"effector"    "effectee"
GeneA         GeneX
GeneB         GeneZ

...etc

Any help is appreciated. Thank you in advance for reading.

Answer 1

[Alex Reynolds]

In conjunction with Neph et al. Circuitry and dynamics of human transcription factor regulatory networks I wrote a graphical tool for exploring regulatory connections of this type.

In this tool, you can pick your tissue or cell type and list of genes, and then click on the "text" button to export a two-column list of regulator-regulated gene relationships, e.g.:

regulator    regulated
AHR          HES1
ARNT         HES1
BACH1        MYB
CBFB         SPI1
CDX1         HES1
CDX2         HES1
CEBPA        TAL1
...

The regulator-regulated relationship indicates if a "regulator" TF binds to a "regulated" gene's promoter region.

For speed, the default setting is to show networks for relationships only between specified genes. You can click on the "both" radio button in the "TF regulatory interactions" row to show all relationships between specified genes and all other genes one level deep.

Further, you can click on the "detail" button to enable the interactions between the set of other genes. Once the interface finishes redrawing the network with the level of detail you want, you can click on the "text" button again to export another list, but this time with all additional genes and relationships.

If you want the complete set without going through visualization, there is a tarball link available via the "about" button.

[Tom A]

Perfect! Thank you Alex.

[gpatters.uh]

I believe for the complete set of interactions the columns are reversed: regulated, regulator. The corresponding README.txt correctly points this out, but I thought it was worth mentioning here as well.

The file genes-regulate-genes.txt contains two columns of gene names. The gene in the first column is bound (i.e., contains a DNaseI footprint in proximal regulatory DNA) corresponding to the second column's TF gene product.

Thanks for the great resource!

Answer 2

[PoGibas]

You can try IntAct from EBI - database system and analysis tools for molecular interaction data (it provides data as you want "Molecule A & Molecule B").

Select organism of interest (advanced search), search and download data. Or you can download entire database.