Literature DB >> 25416956

A proteome-scale map of the human interactome network.

Thomas Rolland1, Murat Taşan2, Benoit Charloteaux1, Samuel J Pevzner3, Quan Zhong4, Nidhi Sahni1, Song Yi1, Irma Lemmens5, Celia Fontanillo6, Roberto Mosca7, Atanas Kamburov1, Susan D Ghiassian8, Xinping Yang1, Lila Ghamsari1, Dawit Balcha1, Bridget E Begg1, Pascal Braun1, Marc Brehme1, Martin P Broly1, Anne-Ruxandra Carvunis1, Dan Convery-Zupan1, Roser Corominas9, Jasmin Coulombe-Huntington10, Elizabeth Dann1, Matija Dreze1, Amélie Dricot1, Changyu Fan1, Eric Franzosa10, Fana Gebreab1, Bryan J Gutierrez1, Madeleine F Hardy1, Mike Jin1, Shuli Kang9, Ruth Kiros1, Guan Ning Lin9, Katja Luck1, Andrew MacWilliams1, Jörg Menche8, Ryan R Murray1, Alexandre Palagi1, Matthew M Poulin1, Xavier Rambout11, John Rasla1, Patrick Reichert1, Viviana Romero1, Elien Ruyssinck5, Julie M Sahalie1, Annemarie Scholz1, Akash A Shah1, Amitabh Sharma8, Yun Shen1, Kerstin Spirohn1, Stanley Tam1, Alexander O Tejeda1, Shelly A Trigg1, Jean-Claude Twizere11, Kerwin Vega1, Jennifer Walsh1, Michael E Cusick1, Yu Xia10, Albert-László Barabási12, Lilia M Iakoucheva9, Patrick Aloy13, Javier De Las Rivas6, Jan Tavernier5, Michael A Calderwood1, David E Hill1, Tong Hao1, Frederick P Roth14, Marc Vidal15.   

Abstract

Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ?14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ?30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a "broader" human interactome network than currently appreciated. The map also uncovers significant interconnectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high-quality interactome models will help "connect the dots" of the genomic revolution.

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Year:  2014        PMID: 25416956      PMCID: PMC4266588          DOI: 10.1016/j.cell.2014.10.050

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  56 in total

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Journal:  Nat Genet       Date:  2012-11-11       Impact factor: 38.330

2.  A census of human soluble protein complexes.

Authors:  Pierre C Havugimana; G Traver Hart; Tamás Nepusz; Haixuan Yang; Andrei L Turinsky; Zhihua Li; Peggy I Wang; Daniel R Boutz; Vincent Fong; Sadhna Phanse; Mohan Babu; Stephanie A Craig; Pingzhao Hu; Cuihong Wan; James Vlasblom; Vaqaar-un-Nisa Dar; Alexandr Bezginov; Gregory W Clark; Gabriel C Wu; Shoshana J Wodak; Elisabeth R M Tillier; Alberto Paccanaro; Edward M Marcotte; Andrew Emili
Journal:  Cell       Date:  2012-08-31       Impact factor: 41.582

3.  Design and application of a cytokine-receptor-based interaction trap.

Authors:  S Eyckerman; A Verhee; J V der Heyden; I Lemmens; X V Ostade; J Vandekerckhove; J Tavernier
Journal:  Nat Cell Biol       Date:  2001-12       Impact factor: 28.824

4.  Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma.

Authors:  Karen M Mann; Jerrold M Ward; Christopher Chin Kuan Yew; Anne Kovochich; David W Dawson; Michael A Black; Benjamin T Brett; Todd E Sheetz; Adam J Dupuy; David K Chang; Andrew V Biankin; Nicola Waddell; Karin S Kassahn; Sean M Grimmond; Alistair G Rust; David J Adams; Nancy A Jenkins; Neal G Copeland
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-15       Impact factor: 11.205

5.  Structure-based prediction of protein-protein interactions on a genome-wide scale.

Authors:  Qiangfeng Cliff Zhang; Donald Petrey; Lei Deng; Li Qiang; Yu Shi; Chan Aye Thu; Brygida Bisikirska; Celine Lefebvre; Domenico Accili; Tony Hunter; Tom Maniatis; Andrea Califano; Barry Honig
Journal:  Nature       Date:  2012-09-30       Impact factor: 49.962

6.  Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.

Authors:  Orit Rozenblatt-Rosen; Rahul C Deo; Megha Padi; Guillaume Adelmant; Michael A Calderwood; Thomas Rolland; Miranda Grace; Amélie Dricot; Manor Askenazi; Maria Tavares; Samuel J Pevzner; Fieda Abderazzaq; Danielle Byrdsong; Anne-Ruxandra Carvunis; Alyce A Chen; Jingwei Cheng; Mick Correll; Melissa Duarte; Changyu Fan; Mariet C Feltkamp; Scott B Ficarro; Rachel Franchi; Brijesh K Garg; Natali Gulbahce; Tong Hao; Amy M Holthaus; Robert James; Anna Korkhin; Larisa Litovchick; Jessica C Mar; Theodore R Pak; Sabrina Rabello; Renee Rubio; Yun Shen; Saurav Singh; Jennifer M Spangle; Murat Tasan; Shelly Wanamaker; James T Webber; Jennifer Roecklein-Canfield; Eric Johannsen; Albert-László Barabási; Rameen Beroukhim; Elliott Kieff; Michael E Cusick; David E Hill; Karl Münger; Jarrod A Marto; John Quackenbush; Frederick P Roth; James A DeCaprio; Marc Vidal
Journal:  Nature       Date:  2012-07-26       Impact factor: 49.962

7.  PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse.

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Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

8.  The IntAct molecular interaction database in 2012.

Authors:  Samuel Kerrien; Bruno Aranda; Lionel Breuza; Alan Bridge; Fiona Broackes-Carter; Carol Chen; Margaret Duesbury; Marine Dumousseau; Marc Feuermann; Ursula Hinz; Christine Jandrasits; Rafael C Jimenez; Jyoti Khadake; Usha Mahadevan; Patrick Masson; Ivo Pedruzzi; Eric Pfeiffenberger; Pablo Porras; Arathi Raghunath; Bernd Roechert; Sandra Orchard; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2011-11-24       Impact factor: 16.971

9.  The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Authors:  Jordi Barretina; Giordano Caponigro; Nicolas Stransky; Kavitha Venkatesan; Adam A Margolin; Sungjoon Kim; Christopher J Wilson; Joseph Lehár; Gregory V Kryukov; Dmitriy Sonkin; Anupama Reddy; Manway Liu; Lauren Murray; Michael F Berger; John E Monahan; Paula Morais; Jodi Meltzer; Adam Korejwa; Judit Jané-Valbuena; Felipa A Mapa; Joseph Thibault; Eva Bric-Furlong; Pichai Raman; Aaron Shipway; Ingo H Engels; Jill Cheng; Guoying K Yu; Jianjun Yu; Peter Aspesi; Melanie de Silva; Kalpana Jagtap; Michael D Jones; Li Wang; Charles Hatton; Emanuele Palescandolo; Supriya Gupta; Scott Mahan; Carrie Sougnez; Robert C Onofrio; Ted Liefeld; Laura MacConaill; Wendy Winckler; Michael Reich; Nanxin Li; Jill P Mesirov; Stacey B Gabriel; Gad Getz; Kristin Ardlie; Vivien Chan; Vic E Myer; Barbara L Weber; Jeff Porter; Markus Warmuth; Peter Finan; Jennifer L Harris; Matthew Meyerson; Todd R Golub; Michael P Morrissey; William R Sellers; Robert Schlegel; Levi A Garraway
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

10.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962

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Authors:  Handan Acar; Ravand Samaeekia; Mathew R Schnorenberg; Dibyendu K Sasmal; Jun Huang; Matthew V Tirrell; James L LaBelle
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Authors:  Xiu-Lei Mo; Yin Luo; Andrei A Ivanov; Rina Su; Jonathan J Havel; Zenggang Li; Fadlo R Khuri; Yuhong Du; Haian Fu
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Authors:  Byung Hak Ha; Elizabeth M Morse; Benjamin E Turk; Titus J Boggon
Journal:  J Biol Chem       Date:  2015-04-08       Impact factor: 5.157

6.  NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.

Authors:  Jianguo Xia; Erin E Gill; Robert E W Hancock
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7.  Pericellular regulation of prostate cancer expressed kallikrein-related peptidases and matrix metalloproteinases by cell surface serine proteases.

Authors:  Janet C Reid; Admire Matsika; Claire M Davies; Yaowu He; Amy Broomfield; Nigel C Bennett; Viktor Magdolen; Bhuvana Srinivasan; Judith A Clements; John D Hooper
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8.  Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions.

Authors:  Christopher J Lord; Niall Quinn; Colm J Ryan
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9.  Widespread macromolecular interaction perturbations in human genetic disorders.

Authors:  Nidhi Sahni; Song Yi; Mikko Taipale; Juan I Fuxman Bass; Jasmin Coulombe-Huntington; Fan Yang; Jian Peng; Jochen Weile; Georgios I Karras; Yang Wang; István A Kovács; Atanas Kamburov; Irina Krykbaeva; Mandy H Lam; George Tucker; Vikram Khurana; Amitabh Sharma; Yang-Yu Liu; Nozomu Yachie; Quan Zhong; Yun Shen; Alexandre Palagi; Adriana San-Miguel; Changyu Fan; Dawit Balcha; Amelie Dricot; Daniel M Jordan; Jennifer M Walsh; Akash A Shah; Xinping Yang; Ani K Stoyanova; Alex Leighton; Michael A Calderwood; Yves Jacob; Michael E Cusick; Kourosh Salehi-Ashtiani; Luke J Whitesell; Shamil Sunyaev; Bonnie Berger; Albert-László Barabási; Benoit Charloteaux; David E Hill; Tong Hao; Frederick P Roth; Yu Xia; Albertha J M Walhout; Susan Lindquist; Marc Vidal
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10.  Phenotypic Screening of Chemical Libraries Enriched by Molecular Docking to Multiple Targets Selected from Glioblastoma Genomic Data.

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Journal:  ACS Chem Biol       Date:  2020-05-21       Impact factor: 5.100

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