https://string-db.org/
(2000) a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations

https://omictools.com/clr-tool
(2007) Infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles.

BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies
Author links open overlay
https://doi.org/10.1016/j.ajhg.2010.07.021

Detecting gene-gene interactions using support vector machines with L1 penalty
https://doi-org.ezproxy.lib.ucalgary.ca/10.1109/BIBMW.2010.5703819

Detecting gene–gene interactions that underlie human diseases
Nature Reviews Genetics volume 10, pages 392–404 (2009)

https://genemania.org/
(2010) finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity

http://www.geneticinteractions.org/research.html
To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.