NDLI: Identifying protein function and functional links based on large-scale co-occurrence patterns.

Content Provider	Directory of Open Access Journals (DOAJ)
Author	Zohar Pasternak Noam Chapnik Roy Yosef Naama M. Kopelman Edouard Jurkevitch Elad Segev
Abstract	ObjectiveThe vast majority of known proteins have not been experimentally tested even at the level of measuring their expression, and the function of many proteins remains unknown. In order to decipher protein function and examine functional associations, we developed "Cliquely", a software tool based on the exploration of co-occurrence patterns.Computational modelUsing a set of more than 23 million proteins divided into 404,947 orthologous clusters, we explored the co-occurrence graph of 4,742 fully sequenced genomes from the three domains of life. Edge weights in this graph represent co-occurrence probabilities. We use the Bron-Kerbosch algorithm to detect maximal cliques in this graph, fully-connected subgraphs that represent meaningful biological networks from different functional categories.Main resultsWe demonstrate that Cliquely can successfully identify known networks from various pathways, including nitrogen fixation, glycolysis, methanogenesis, mevalonate and ribosome proteins. Identifying the virulence-associated type III secretion system (T3SS) network, Cliquely also added 13 previously uncharacterized novel proteins to the T3SS network, demonstrating the strength of this approach. Cliquely is freely available and open source. Users can employ the tool to explore co-occurrence networks using a protein of interest and a customizable level of stringency, either for the entire dataset or for a one of the three domains-Archaea, Bacteria, or Eukarya.
e-ISSN	19326203
DOI	10.1371/journal.pone.0264765
Journal	PLoS ONE
Issue Number	3
Volume Number	17
Language	English
Publisher	Public Library of Science (PLoS)
Publisher Date	2022-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Medicine Science
Content Type	Text
Resource Type	Article

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