Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases? So far, I found String but it is does not have enough proteins for my purposes. Are there such databases with more entries? I'm still open to any proposition of the disease to choose from . the most important part is the volume of data . And how can I get the annotation of each protein of the extracted network from Uniprot ?
There is a bunch of decent protein-protein interaction databases: Biocarta, BioGrid, DIP, InnateDB, IntAct, MINT, PPID. Some of them aren't available now, but you can download datasets from the Expression2Kinases download page because they are integrated into X2K pipeline as part of Genes2Networks analysis. If you need more proteins, you can submit your list of proteins to X2K and use G2N analysis to connect enriched transcription factors through known protein-protein interactions.
Also, the new dataset called hu.MAP was published recently. It is a dataset of human protein-protein interactions determined by over 9,000 mass spectrometry experiments performed by the Marcotte Lab from UT Austin. A paper that describes the hu.MAP project is available on Biorxiv.
BioPlex (biophysical interactions of ORFeome-based complexes) is another database with experimental verification. Authors describe it as a network that is
the result of creating thousands of cell lines with each expressing a tagged version of a protein from the ORFeome collection. Immunopurification of the tagged protein and detection of associated proteins by mass spectrometry are the building blocks of the network. The overarching project goal is to determine protein interactions for every member of the collection.