How to predict Zinc Finger's putative gene targets?

You can try String

https://string-db.org

Regards

In addition to STRING also worth checking out Reactome:

https://reactome.org/content/query?q=zinc+finger-containing&species=Homo+sapiens&species=Entries+without+species&cluster=true

Hey O'Callaghan!

String is a very good tool, as well Reactome... But you can try https://thebiogrid.org/ too, or use all and merge it in cytoscape.

Best regards,

Leite

Thank you all for your answers,

All STRING, Reactome, and BioGrid are powerful resources for protein-protein interaction analysis and networking. However, my interest is mainly in protein-DNA interaction. As it is about a zinc finger protein, and those proteins interact with the DNA in a sequence-specific manner, I sought to predict which genes could my protein of interest interact with (at epigenetic level).

After some attempts, I could infer a DNA target pattern as a Position Weight Matrix of the DNA sequence theoretically recognized by my protein of interest, with http://zf.princeton.edu/logoMain.php . Then, using fimo (http://meme-suite.org/tools/fimo) I could extract the genome coordinates where my DNA pattern maps, and finally, with Biomart (http://www.ensambl.org/biomart), I generate a list of genes mapping within the given coordinates. Considering that zinc finger endogenous proteins may act within the promoter region, I expand the predicted coordinates 500 bp in both directions, just to attempt including nearby genes.

Hope it will be useful for others with same propose.