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.
2 answers
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.
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!
•
written
by
gpatters.uh •
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.
Log in to answer this question.