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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 ?

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    $\begingroup$ Welcome to Biology.SE. I edited your question to make it more clear. Please feel free to further edit. Thanks! $\endgroup$ – AlexDeLarge May 16 '17 at 9:05
  • $\begingroup$ The String database is one of the best available, how many proteins do you need? (consider that the human genome is predicted to have around 25k protein-coding genes) $\endgroup$ – alec_djinn May 16 '17 at 9:41
  • $\begingroup$ @alec_djinn I need for about 5k or 6k proteins for alzheimer or cancer but i don't know how to retreive that quantity at once $\endgroup$ – A M May 16 '17 at 9:45
  • $\begingroup$ @AM I can't find the exact number of entries for the human proteins, maybe you should contact them, 5k sounds reasonable, I would expect them to have it. If not, maybe you can integrate with other mammalian proteins. As far I know, STRING is the most complete you can find now. $\endgroup$ – alec_djinn May 16 '17 at 9:54
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    $\begingroup$ @AM please edit your question and clarify your needs. Do you want to limit the results to binary interactions only? Are you also interested in non-direct interactions like forming part of the same complex? Do you want only experimentally verified interactions or also those inferred by electronic annotations? Do you have a list of proteins of interest? Please add more details. $\endgroup$ – terdon May 17 '17 at 16:58
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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.

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  • $\begingroup$ I have checked IntAct, and it kind of offers what I've been looking for , I'm wondering If there is a way to extract all the associated proteins' annotations from uniprot . because I need to get all the annotations of every protein contained in the dataset $\endgroup$ – A M May 19 '17 at 18:36

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