Gene-Gene\Protein-Protein Interaction Network — Tools

  1. Cytoscape — Agi­lent Lit­er­a­ture Search
  2. STRING:
    The many func­tion­al part­ner­ships and inter­ac­tions that occur between pro­teins are at the core of cel­lu­lar pro­cess­ing and their sys­tem­at­ic char­ac­ter­i­za­tion helps to provide con­text in mol­e­c­u­lar sys­tems biol­o­gy. How­ev­er, known and pre­dict­ed inter­ac­tions are scat­tered over mul­ti­ple resources, and the avail­able data exhibit notable dif­fer­ences in terms of qual­i­ty and com­plete­ness. The STRING data­base (http://string-db.org) aims to provide a crit­i­cal assess­ment and inte­gra­tion of protein–protein inter­ac­tions, includ­ing direct (phys­i­cal) as well as indi­rect (func­tion­al) asso­ci­a­tions. The new ver­sion 10.0 of STRING cov­ers more than 2000 organ­isms, which has neces­si­tat­ed nov­el, scal­able algo­rithms for trans­fer­ring inter­ac­tion infor­ma­tion between organ­isms. For this pur­pose, we have intro­duced hier­ar­chi­cal and self-con­sis­tent orthol­o­gy anno­ta­tions for all inter­act­ing pro­teins, group­ing the pro­teins into fam­i­lies at var­i­ous lev­els of phy­lo­ge­net­ic res­o­lu­tion. Fur­ther improve­ments in ver­sion 10.0 include a com­plete­ly redesigned pre­dic­tion pipeline for infer­ring protein–protein asso­ci­a­tions from co-expres­sion data, an API inter­face for the R com­put­ing envi­ron­ment and improved sta­tis­ti­cal analy­sis for enrich­ment tests in user-pro­vid­ed net­works.
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