2
$\begingroup$

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? Thanks in advance!

$\endgroup$
  • $\begingroup$ Could you add the specific KEGG identifier? $\endgroup$ – James Feb 23 '16 at 7:41
  • $\begingroup$ @James As an example for some protein? $\endgroup$ – L. Bird Feb 23 '16 at 10:33
  • $\begingroup$ There are several reasons why you might not be able to find the references. You might not know what you're looking for or perhaps the specific protein is unreferenced. It would be useful to start with your example and work from there. $\endgroup$ – James Feb 24 '16 at 6:10
1
$\begingroup$

You can try to use IntAct Molecular Interaction Database. The data in this database is based on:

  • data from the literature or from direct data depositions by expert curators
  • <300k binary interactions in 2011 developed by the EBI's Proteomics Services Team
  • recent reference: Aranda et al. '10

This is also mentioned in the summary of the Aranda et al.'10 article:

IntAct is an open-source, open data molecular interaction database and toolkit. Data is abstracted from the literature or from direct data depositions by expert curators following a deep annotation model providing a high level of detail. As of September 2009, IntAct contains over 200.000 curated binary interaction evidences. In response to the growing data volume and user requests, IntAct now provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available

Further you can use the Evidence tab in String(I assume you have already tried this but in the case you did not):
enter image description here
You can then click on Experiments, then something like this will show up: enter image description here
You can see how (e.g. Reconstituted Complex assay) and you can see from which article this interaction is coming from if you click on an item in the table:
enter image description here

$\endgroup$
-1
$\begingroup$

STRING database shows the protein-protein interaction network and scores according to the presence and absence of experimental verification which can be protease assay, bait coimmunoprecipitation, western assay etc.

if you need further confirmation you should read as much as related articles as possible related to APP.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.