Literature DB >> 17845715

Coverage and error models of protein-protein interaction data by directed graph analysis.

Tony Chiang1, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber.   

Abstract

Using a directed graph model for bait to prey systems and a multinomial error model, we assessed the error statistics in all published large-scale datasets for Saccharomyces cerevisiae and characterized them by three traits: the set of tested interactions, artifacts that lead to false-positive or false-negative observations, and estimates of the stochastic error rates that affect the data. These traits provide a prerequisite for the estimation of the protein interactome and its modules.

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Year:  2007        PMID： 17845715      PMCID： PMC2375024          DOI： 10.1186/gb-2007-8-9-r186

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  41 in total

1.  On the structure of protein-protein interaction networks.

Authors:  A Thomas; R Cannings; N A M Monk; C Cannings
Journal:  Biochem Soc Trans       Date:  2003-12       Impact factor: 5.407

2.  Increasing specificity in high-throughput yeast two-hybrid experiments.

Authors:  Pierre-Olivier Vidalain; Mike Boxem; Hui Ge; Siming Li; Marc Vidal
Journal:  Methods       Date:  2004-04       Impact factor: 3.608

3.  Towards a proteome-scale map of the human protein-protein interaction network.

Authors:  Jean-François Rual; Kavitha Venkatesan; Tong Hao; Tomoko Hirozane-Kishikawa; Amélie Dricot; Ning Li; Gabriel F Berriz; Francis D Gibbons; Matija Dreze; Nono Ayivi-Guedehoussou; Niels Klitgord; Christophe Simon; Mike Boxem; Stuart Milstein; Jennifer Rosenberg; Debra S Goldberg; Lan V Zhang; Sharyl L Wong; Giovanni Franklin; Siming Li; Joanna S Albala; Janghoo Lim; Carlene Fraughton; Estelle Llamosas; Sebiha Cevik; Camille Bex; Philippe Lamesch; Robert S Sikorski; Jean Vandenhaute; Huda Y Zoghbi; Alex Smolyar; Stephanie Bosak; Reynaldo Sequerra; Lynn Doucette-Stamm; Michael E Cusick; David E Hill; Frederick P Roth; Marc Vidal
Journal:  Nature       Date:  2005-09-28       Impact factor: 49.962

4.  Functional organization of the yeast proteome by systematic analysis of protein complexes.

Authors:  Anne-Claude Gavin; Markus Bösche; Roland Krause; Paola Grandi; Martina Marzioch; Andreas Bauer; Jörg Schultz; Jens M Rick; Anne-Marie Michon; Cristina-Maria Cruciat; Marita Remor; Christian Höfert; Malgorzata Schelder; Miro Brajenovic; Heinz Ruffner; Alejandro Merino; Karin Klein; Manuela Hudak; David Dickson; Tatjana Rudi; Volker Gnau; Angela Bauch; Sonja Bastuck; Bettina Huhse; Christina Leutwein; Marie-Anne Heurtier; Richard R Copley; Angela Edelmann; Erich Querfurth; Vladimir Rybin; Gerard Drewes; Manfred Raida; Tewis Bouwmeester; Peer Bork; Bertrand Seraphin; Bernhard Kuster; Gitte Neubauer; Giulio Superti-Furga
Journal:  Nature       Date:  2002-01-10       Impact factor: 49.962

5.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

Authors:  P M Sharp; W H Li
Journal:  Nucleic Acids Res       Date:  1987-02-11       Impact factor: 16.971

6.  A comprehensive two-hybrid analysis to explore the yeast protein interactome.

Authors:  T Ito; T Chiba; R Ozawa; M Yoshida; M Hattori; Y Sakaki
Journal:  Proc Natl Acad Sci U S A       Date:  2001-03-13       Impact factor: 11.205

7.  High-definition macromolecular composition of yeast RNA-processing complexes.

Authors:  Nevan J Krogan; Wen-Tao Peng; Gerard Cagney; Mark D Robinson; Robin Haw; Gouqing Zhong; Xinghua Guo; Xin Zhang; Veronica Canadien; Dawn P Richards; Bryan K Beattie; Atanas Lalev; Wen Zhang; Armaity P Davierwala; Sanie Mnaimneh; Andrei Starostine; Aaron P Tikuisis; Jorg Grigull; Nira Datta; James E Bray; Timothy R Hughes; Andrew Emili; Jack F Greenblatt
Journal:  Mol Cell       Date:  2004-01-30       Impact factor: 17.970

8.  A map of the interactome network of the metazoan C. elegans.

Authors:  Siming Li; Christopher M Armstrong; Nicolas Bertin; Hui Ge; Stuart Milstein; Mike Boxem; Pierre-Olivier Vidalain; Jing-Dong J Han; Alban Chesneau; Tong Hao; Debra S Goldberg; Ning Li; Monica Martinez; Jean-François Rual; Philippe Lamesch; Lai Xu; Muneesh Tewari; Sharyl L Wong; Lan V Zhang; Gabriel F Berriz; Laurent Jacotot; Philippe Vaglio; Jérôme Reboul; Tomoko Hirozane-Kishikawa; Qianru Li; Harrison W Gabel; Ahmed Elewa; Bridget Baumgartner; Debra J Rose; Haiyuan Yu; Stephanie Bosak; Reynaldo Sequerra; Andrew Fraser; Susan E Mango; William M Saxton; Susan Strome; Sander Van Den Heuvel; Fabio Piano; Jean Vandenhaute; Claude Sardet; Mark Gerstein; Lynn Doucette-Stamm; Kristin C Gunsalus; J Wade Harper; Michael E Cusick; Frederick P Roth; David E Hill; Marc Vidal
Journal:  Science       Date:  2004-01-02       Impact factor: 47.728

9.  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

10.  Assigning function to yeast proteins by integration of technologies.

Authors:  Tony R Hazbun; Lars Malmström; Scott Anderson; Beth J Graczyk; Bethany Fox; Michael Riffle; Bryan A Sundin; J Derringer Aranda; W Hayes McDonald; Chun-Hwei Chiu; Brian E Snydsman; Phillip Bradley; Eric G D Muller; Stanley Fields; David Baker; John R Yates; Trisha N Davis
Journal:  Mol Cell       Date:  2003-12       Impact factor: 17.970
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  16 in total

Review 1.  Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.

Authors:  Bram Stynen; Hélène Tournu; Jan Tavernier; Patrick Van Dijck
Journal:  Microbiol Mol Biol Rev       Date:  2012-06       Impact factor: 11.056

2.  A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor.

Authors:  Tony Chiang; Denise Scholtens
Journal:  Nat Protoc       Date:  2009-03-26       Impact factor: 13.491

Review 3.  Protein interaction predictions from diverse sources.

Authors:  Yin Liu; Inyoung Kim; Hongyu Zhao
Journal:  Drug Discov Today       Date:  2008-03-06       Impact factor: 7.851

4.  From evidence to inference: probing the evolution of protein interaction networks.

Authors:  Oliver Ratmann; Carsten Wiuf; John W Pinney
Journal:  HFSP J       Date:  2009-10-19

Review 5.  Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments.

Authors:  Alexey I Nesvizhskii
Journal:  Proteomics       Date:  2012-05       Impact factor: 3.984

6.  High throughput interaction data reveals degree conservation of hub proteins.

Authors:  A Fox; D Taylor; D K Slonim
Journal:  Pac Symp Biocomput       Date:  2009

7.  A portrait of copy-number polymorphism in Drosophila melanogaster.

Authors:  Erik B Dopman; Daniel L Hartl
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-04       Impact factor: 11.205

8.  Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.

Authors:  Swapnil R Chhabra; Marcin P Joachimiak; Christopher J Petzold; Grant M Zane; Morgan N Price; Sonia A Reveco; Veronica Fok; Alyssa R Johanson; Tanveer S Batth; Mary Singer; John-Marc Chandonia; Dominique Joyner; Terry C Hazen; Adam P Arkin; Judy D Wall; Anup K Singh; Jay D Keasling
Journal:  PLoS One       Date:  2011-06-28       Impact factor: 3.240

9.  Triangle network motifs predict complexes by complementing high-error interactomes with structural information.

Authors:  Bill Andreopoulos; Christof Winter; Dirk Labudde; Michael Schroeder
Journal:  BMC Bioinformatics       Date:  2009-06-27       Impact factor: 3.169

10.  An experimentally derived confidence score for binary protein-protein interactions.

Authors:  Pascal Braun; Murat Tasan; Matija Dreze; Miriam Barrios-Rodiles; Irma Lemmens; Haiyuan Yu; Julie M Sahalie; Ryan R Murray; Luba Roncari; Anne-Sophie de Smet; Kavitha Venkatesan; Jean-François Rual; Jean Vandenhaute; Michael E Cusick; Tony Pawson; David E Hill; Jan Tavernier; Jeffrey L Wrana; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2008-12-07       Impact factor: 28.547
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