Literature DB >> 26564972

MIPCE: an MI-based protein complex extraction technique.

Priyakshi Mahanta1, Dhruba Kr Bhattacharyya, Ashish Ghosh.   

Abstract

Protein-protein interaction (PPI) networks are believed to be important sources of information related to biological processes and complex metabolic functions of the cell. Identifying protein complexes is of great importance for understanding cellular organization and functions of organisms. In this work, a method is proposed, referred to as MIPCE, to find protein complexes in a PPI network based on mutual information.MIPCE has been biologically validated by GO-based score and satisfactory results have been obtained. We have also compared our method with some wellknown methods and obtained better results in terms of various parameters such as precession, recall and F-measure.

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Year:  2015        PMID: 26564972     DOI: 10.1007/s12038-015-9553-1

Source DB:  PubMed          Journal:  J Biosci        ISSN: 0250-5991            Impact factor:   1.826


  16 in total

1.  Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements.

Authors:  A J Butte; I S Kohane
Journal:  Pac Symp Biocomput       Date:  2000

2.  Proteome survey reveals modularity of the yeast cell machinery.

Authors:  Anne-Claude Gavin; Patrick Aloy; Paola Grandi; Roland Krause; Markus Boesche; Martina Marzioch; Christina Rau; Lars Juhl Jensen; Sonja Bastuck; Birgit Dümpelfeld; Angela Edelmann; Marie-Anne Heurtier; Verena Hoffman; Christian Hoefert; Karin Klein; Manuela Hudak; Anne-Marie Michon; Malgorzata Schelder; Markus Schirle; Marita Remor; Tatjana Rudi; Sean Hooper; Andreas Bauer; Tewis Bouwmeester; Georg Casari; Gerard Drewes; Gitte Neubauer; Jens M Rick; Bernhard Kuster; Peer Bork; Robert B Russell; Giulio Superti-Furga
Journal:  Nature       Date:  2006-01-22       Impact factor: 49.962

3.  CFinder: locating cliques and overlapping modules in biological networks.

Authors:  Balázs Adamcsek; Gergely Palla; Illés J Farkas; Imre Derényi; Tamás Vicsek
Journal:  Bioinformatics       Date:  2006-02-10       Impact factor: 6.937

4.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.

Authors:  Ioannis Xenarios; Lukasz Salwínski; Xiaoqun Joyce Duan; Patrick Higney; Sul-Min Kim; David Eisenberg
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  FUMET: a fuzzy network module extraction technique for gene expression data.

Authors:  Priyakshi Mahanta; Hasin Afzal Ahmed; Dhruba Kumar Bhattacharyya; Ashish Ghosh
Journal:  J Biosci       Date:  2014-06       Impact factor: 1.826

6.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Authors:  Nevan J Krogan; Gerard Cagney; Haiyuan Yu; Gouqing Zhong; Xinghua Guo; Alexandr Ignatchenko; Joyce Li; Shuye Pu; Nira Datta; Aaron P Tikuisis; Thanuja Punna; José M Peregrín-Alvarez; Michael Shales; Xin Zhang; Michael Davey; Mark D Robinson; Alberto Paccanaro; James E Bray; Anthony Sheung; Bryan Beattie; Dawn P Richards; Veronica Canadien; Atanas Lalev; Frank Mena; Peter Wong; Andrei Starostine; Myra M Canete; James Vlasblom; Samuel Wu; Chris Orsi; Sean R Collins; Shamanta Chandran; Robin Haw; Jennifer J Rilstone; Kiran Gandi; Natalie J Thompson; Gabe Musso; Peter St Onge; Shaun Ghanny; Mandy H Y Lam; Gareth Butland; Amin M Altaf-Ul; Shigehiko Kanaya; Ali Shilatifard; Erin O'Shea; Jonathan S Weissman; C James Ingles; Timothy R Hughes; John Parkinson; Mark Gerstein; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2006-03-22       Impact factor: 49.962

7.  An automated method for finding molecular complexes in large protein interaction networks.

Authors:  Gary D Bader; Christopher W V Hogue
Journal:  BMC Bioinformatics       Date:  2003-01-13       Impact factor: 3.169

8.  Development and implementation of an algorithm for detection of protein complexes in large interaction networks.

Authors:  Md Altaf-Ul-Amin; Yoko Shinbo; Kenji Mihara; Ken Kurokawa; Shigehiko Kanaya
Journal:  BMC Bioinformatics       Date:  2006-04-14       Impact factor: 3.169

9.  A core-attachment based method to detect protein complexes in PPI networks.

Authors:  Min Wu; Xiaoli Li; Chee-Keong Kwoh; See-Kiong Ng
Journal:  BMC Bioinformatics       Date:  2009-06-02       Impact factor: 3.169

10.  Evaluation of gene-expression clustering via mutual information distance measure.

Authors:  Ido Priness; Oded Maimon; Irad Ben-Gal
Journal:  BMC Bioinformatics       Date:  2007-03-30       Impact factor: 3.169

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