Protein-protein interactions search (STRING DB)
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5.2 years ago
leriapingui ▴ 20

I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant amount of interactors have only "Database" confirmation (mostly relaying on Reactome and KEGG data). Searching in these db's gives me neither article nor even the presence of these proteins in one pathway (what's weird). How can I obtain the data?

P.S. If it's possible to use API for getting all the articles -- that'd be great.

Thanks in advance!

interaction string reactome • 2.5k views
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Hi, I don't have an answer to your query but I will appreciate if you guide me how to use STRINGdb to find all the interactions of a particular protein. Thanks

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can u please tell me how did you use stringdb package to retrieve data for protein protein interactions

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4.3 years ago
Chun-Jie Liu ▴ 280

The following information is old fashioned as @cdsouthan informing me that HPRD should not be recommended. The data is not updated since 04-13-10.


Original answer

If you just want to get all PPI by the experiments, you can download data from BioGRID and HPRD. Both databases curated evidence of protein-protein interaction and paper PubMed ID.

The HPRD mainly focus on the human protein interaction by ONLY reviewing the papers. If you do research on human. I recommend HPRD database.

  • Are you using any literature mining algorithm?

We are not using any literature mining program. Our trained biologists read and interpret each and every paper related to the molecule of interest.

  • Why did you decide against automation?

We simply realized that our method of manual extraction is far more efficient and accurate than any literature mining algorithm.

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4.3 years ago
cdsouthan ★ 1.8k

You may get more current results from the EBI Intact database that updates monthly

It is one of the sources parsed by STITCH and STRING. They even have a special Alzheimer's set

Note also that the UniProt APP entry has a 44-protein interaction matrix

STRING was last updated in Apr 16, 2016

n.b. beware of HPRD suggested (in good faith I'm sure) above. The download page is frozen at 2010 and so is definitely not to be recommended.

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Thanks for your information.

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