I want to find the experimentally verified interactions. For example, when we find the PPI, we can use the databases, such as BioGrid, IntAct....Are there such databases for gene-gene interaction ?
The protein-protein Interaction databases are there because proteins interact physically, genes as DNA or RNA fragment donot normally interact , they exist as gene-fusions or chimeric transcripts, and there are databases for cancer or stem cells , if I remember correctly, but I am not sure that you are searching for same.
May be you are looking for something like transcriptional regulatory network , for which I would recommend you to use cytoscape , and get your own on the basis of your data.
the interactome database devoleped by the EMBL group based in Heidelburg is a very comprehensive one. google it for more information.
BioGRID has some of these interactions, listed as 'Genetic' interactions, and if you want to pay, TransFac has databases of transcription factor and TF-motif interactions.
I will concur with Alberto in making use of GeneMANIA though it may be slower with an input gene list of more than 50 genes; if you have such large gene lists, we recommend using a gene list of no more than 100 genes. The fortunate part in this regard is that can apply GeneMANIA Cytoscape plugin which is capable of handling larger gene list. This plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data. The plugin follows the look and feel of the GeneMANIA website, but provides more features for power-users
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