Protein Protein Interaction

Question

[Plasmid]

I am new in protein interaction. I downloaded a interaction file of a protein from BioGrid database. I put this file into Cytoscape to view the interaction. In this case I only observed interaction with central protein. Is there anyway that I can get also interaction among the proteins and interaction with central protein? Are there other database that give me the same result?

Answer 1

[Pierre Lindenbaum]

The STRING Api returns all the interactions between the proteins.

eg. with eif4G1:

as XML:

http://string-db.org/api/psi-mi/interactionsList?identifiers=9606.ENSP00000316879

or as TSV:

http://string-db.org/api/psi-mi-tab/interactionsList?identifiers=9606.ENSP00000316879

	string:9606.ENSP00000316879 string:9606.ENSP00000280892 EIF4G1 EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.999|escore:0.999|dscore:0.9|tscore:0.974
	string:9606.ENSP00000354125 string:9606.ENSP00000310040 EIF3B EIF3F - - - - - taxid:9606 taxid:9606 - - - score:0.999|ascore:0.105|escore:0.986|dscore:0.9|tscore:0.773
	string:9606.ENSP00000362688 string:9606.ENSP00000354125 EIF3I EIF3B - - - - - taxid:9606 taxid:9606 - - - score:0.999|ascore:0.617|escore:0.902|dscore:0.9|tscore:0.876
	string:9606.ENSP00000316879 string:9606.ENSP00000293831 EIF4G1 EIF4A1 - - - - - taxid:9606 taxid:9606 - - - score:0.999|escore:0.994|dscore:0.9|tscore:0.97
	string:9606.ENSP00000354125 string:9606.ENSP00000276682 EIF3B EIF3H - - - - - taxid:9606 taxid:9606 - - - score:0.999|escore:0.973|dscore:0.9|tscore:0.768
	string:9606.ENSP00000362688 string:9606.ENSP00000276682 EIF3I EIF3H - - - - - taxid:9606 taxid:9606 - - - score:0.998|ascore:0.395|escore:0.927|dscore:0.9|tscore:0.748
	string:9606.ENSP00000310040 string:9606.ENSP00000276682 EIF3F EIF3H - - - - - taxid:9606 taxid:9606 - - - score:0.998|ascore:0.29|escore:0.966|dscore:0.9|tscore:0.30301
	string:9606.ENSP00000362688 string:9606.ENSP00000310040 EIF3I EIF3F - - - - - taxid:9606 taxid:9606 - - - score:0.998|ascore:0.439|escore:0.927|dscore:0.9|tscore:0.722
	string:9606.ENSP00000293831 string:9606.ENSP00000280892 EIF4A1 EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.997|escore:0.613|dscore:0.9|tscore:0.942
	string:9606.ENSP00000280892 string:9606.ENSP00000262056 EIF4E EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.997|escore:0.62|dscore:0.9|tscore:0.949
	string:9606.ENSP00000293831 string:9606.ENSP00000262056 EIF4A1 EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.996|dscore:0.9|tscore:0.967
	string:9606.ENSP00000276682 string:9606.ENSP00000262056 EIF3H EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.994|ascore:0.333|escore:0.927|dscore:0.9|tscore:0.065
	string:9606.ENSP00000354125 string:9606.ENSP00000280892 EIF3B EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.993|ascore:0.105|escore:0.808|dscore:0.9|tscore:0.684
	string:9606.ENSP00000280892 string:9606.ENSP00000276682 EIF4E EIF3H - - - - - taxid:9606 taxid:9606 - - - score:0.992|escore:0.927|dscore:0.9|tscore:0.064
	string:9606.ENSP00000310040 string:9606.ENSP00000280892 EIF3F EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.992|escore:0.927|dscore:0.9|tscore:0.064
	string:9606.ENSP00000316879 string:9606.ENSP00000310040 EIF4G1 EIF3F - - - - - taxid:9606 taxid:9606 - - - score:0.992|escore:0.927|dscore:0.9|tscore:0.061
	string:9606.ENSP00000316879 string:9606.ENSP00000276682 EIF4G1 EIF3H - - - - - taxid:9606 taxid:9606 - - - score:0.992|escore:0.927|dscore:0.9|tscore:0.061
	string:9606.ENSP00000310040 string:9606.ENSP00000262056 EIF3F EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.992|escore:0.927|dscore:0.9|tscore:0.065
	string:9606.ENSP00000326381 string:9606.ENSP00000316879 EIF4A2 EIF4G1 - - - - - taxid:9606 taxid:9606 - - - score:0.986|escore:0.66|dscore:0.9|tscore:0.645
	string:9606.ENSP00000316879 string:9606.ENSP00000262056 EIF4G1 EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.986|dscore:0.9|tscore:0.874
	string:9606.ENSP00000354125 string:9606.ENSP00000316879 EIF3B EIF4G1 - - - - - taxid:9606 taxid:9606 - - - score:0.984|ascore:0.171|escore:0.608|dscore:0.9|tscore:0.606
	string:9606.ENSP00000348578 string:9606.ENSP00000316879 G3BP1 EIF4G1 - - - - - taxid:9606 taxid:9606 - - - score:0.977|escore:0.97|tscore:0.289
	string:9606.ENSP00000387911 string:9606.ENSP00000280892 PARN EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.974|dscore:0.9|tscore:0.759
	string:9606.ENSP00000326381 string:9606.ENSP00000276682 EIF4A2 EIF3H - - - - - taxid:9606 taxid:9606 - - - score:0.971|ascore:0.219|escore:0.965|tscore:0.056
	string:9606.ENSP00000326381 string:9606.ENSP00000262056 EIF4A2 EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.966|dscore:0.9|tscore:0.687
	string:9606.ENSP00000387911 string:9606.ENSP00000316879 PARN EIF4G1 - - - - - taxid:9606 taxid:9606 - - - score:0.958|dscore:0.9|tscore:0.613
	string:9606.ENSP00000362688 string:9606.ENSP00000316879 EIF3I EIF4G1 - - - - - taxid:9606 taxid:9606 - - - score:0.957|escore:0.604|dscore:0.9|tscore:0.061
	string:9606.ENSP00000326381 string:9606.ENSP00000280892 EIF4A2 EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.957|escore:0.198|dscore:0.9|tscore:0.534
	string:9606.ENSP00000354125 string:9606.ENSP00000262056 EIF3B EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.952|escore:0.556|dscore:0.9|tscore:0.065
	string:9606.ENSP00000326381 string:9606.ENSP00000310040 EIF4A2 EIF3F - - - - - taxid:9606 taxid:9606 - - - score:0.927|escore:0.927|tscore:0.056
	string:9606.ENSP00000362688 string:9606.ENSP00000262056 EIF3I EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.922|escore:0.268|dscore:0.9|tscore:0.065
	string:9606.ENSP00000362688 string:9606.ENSP00000280892 EIF3I EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.914|ascore:0.2|dscore:0.9|tscore:0.064
	string:9606.ENSP00000326381 string:9606.ENSP00000293831 EIF4A2 EIF4A1 - - - - - taxid:9606 taxid:9606 - - - score:0.904|pscore:0.0147|dscore:0.9|tscore:0.02716
	string:9606.ENSP00000387911 string:9606.ENSP00000262056 PARN EIF4B - - - - - taxid:9606 taxid:9606 - - - score:0.899|dscore:0.9|tscore:0.006
	string:9606.ENSP00000348578 string:9606.ENSP00000280892 G3BP1 EIF4E - - - - - taxid:9606 taxid:9606 - - - score:0.619|escore:0.62
	string:9606.ENSP00000354125 string:9606.ENSP00000293831 EIF3B EIF4A1 - - - - - taxid:9606 taxid:9606 - - - score:0.572|ascore:0.09|escore:0.559|tscore:0.064

view raw biostars-16798.txt hosted with ❤ by GitHub

Answer 2

[B. Arman Aksoy]

You can also download tab-limited dump file for HPRD directly from their website, http://www.hprd.org/download, or you can go with the Pathway Commons normalized SIF exports of various other data sources: http://www.pathwaycommons.org/pc-snapshot/current-release/sif/by_source/

These are huge 'interactome's though; Cytoscape will only build the network in the background but for visualization, you probably have to right click on the network (from the left-side menu) and use the 'create view' option explicitly.

Answer 3

[Woa]

There are some Plugins available for Cytoscape that can add interactions within the selected nodes viz. MIMI, APID2NET and BISOGENET

Cytoscape Plug-In For Retrieving Protein-Protein Interactions