Literature DB >> 27892958

A scored human protein-protein interaction network to catalyze genomic interpretation.

Taibo Li1,2,3, Rasmus Wernersson4,5, Rasmus B Hansen4, Heiko Horn1,2,6, Johnathan Mercer1,2, Greg Slodkowicz5, Christopher T Workman5, Olga Rigina5, Kristoffer Rapacki5, Hans H Stærfeldt5, Søren Brunak7, Thomas S Jensen4, Kasper Lage1,2,6,8.   

Abstract

Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (InWeb_InBioMap, or InWeb_IM) with severalfold more interactions (>500,000) and better functional biological relevance than comparable resources. We illustrate that InWeb_InBioMap enables functional interpretation of >4,700 cancer genomes and genes involved in autism.

Entities:  

Mesh：

Year:  2016        PMID： 27892958      PMCID： PMC5839635          DOI： 10.1038/nmeth.4083

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  44 in total

1.  BIND: the Biomolecular Interaction Network Database.

Authors:  Gary D Bader; Doron Betel; Christopher W V Hogue
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

2.  A human interactome in three quantitative dimensions organized by stoichiometries and abundances.

Authors:  Marco Y Hein; Nina C Hubner; Ina Poser; Jürgen Cox; Nagarjuna Nagaraj; Yusuke Toyoda; Igor A Gak; Ina Weisswange; Jörg Mansfeld; Frank Buchholz; Anthony A Hyman; Matthias Mann
Journal:  Cell       Date:  2015-10-22       Impact factor: 41.582

3.  Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci.

Authors:  Stephan J Sanders; Xin He; A Jeremy Willsey; A Gulhan Ercan-Sencicek; Kaitlin E Samocha; A Ercument Cicek; Michael T Murtha; Vanessa H Bal; Somer L Bishop; Shan Dong; Arthur P Goldberg; Cai Jinlu; John F Keaney; Lambertus Klei; Jeffrey D Mandell; Daniel Moreno-De-Luca; Christopher S Poultney; Elise B Robinson; Louw Smith; Tor Solli-Nowlan; Mack Y Su; Nicole A Teran; Michael F Walker; Donna M Werling; Arthur L Beaudet; Rita M Cantor; Eric Fombonne; Daniel H Geschwind; Dorothy E Grice; Catherine Lord; Jennifer K Lowe; Shrikant M Mane; Donna M Martin; Eric M Morrow; Michael E Talkowski; James S Sutcliffe; Christopher A Walsh; Timothy W Yu; David H Ledbetter; Christa Lese Martin; Edwin H Cook; Joseph D Buxbaum; Mark J Daly; Bernie Devlin; Kathryn Roeder; Matthew W State
Journal:  Neuron       Date:  2015-09-23       Impact factor: 17.173

4.  BioGRID: a general repository for interaction datasets.

Authors:  Chris Stark; Bobby-Joe Breitkreutz; Teresa Reguly; Lorrie Boucher; Ashton Breitkreutz; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

5.  MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.

Authors:  G Launay; R Salza; D Multedo; N Thierry-Mieg; S Ricard-Blum
Journal:  Nucleic Acids Res       Date:  2014-11-06       Impact factor: 16.971

6.  STRING v10: protein-protein interaction networks, integrated over the tree of life.

Authors:  Damian Szklarczyk; Andrea Franceschini; Stefan Wyder; Kristoffer Forslund; Davide Heller; Jaime Huerta-Cepas; Milan Simonovic; Alexander Roth; Alberto Santos; Kalliopi P Tsafou; Michael Kuhn; Peer Bork; Lars J Jensen; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2014-10-28       Impact factor: 16.971

7.  OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

Authors:  Evgenia V Kriventseva; Fredrik Tegenfeldt; Tom J Petty; Robert M Waterhouse; Felipe A Simão; Igor A Pozdnyakov; Panagiotis Ioannidis; Evgeny M Zdobnov
Journal:  Nucleic Acids Res       Date:  2014-11-26       Impact factor: 16.971

8.  eggNOG v4.0: nested orthology inference across 3686 organisms.

Authors:  Sean Powell; Kristoffer Forslund; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth; Jaime Huerta-Cepas; Toni Gabaldón; Thomas Rattei; Chris Creevey; Michael Kuhn; Lars J Jensen; Christian von Mering; Peer Bork
Journal:  Nucleic Acids Res       Date:  2013-12-01       Impact factor: 16.971

9.  Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics.

Authors:  Alicia Lundby; Elizabeth J Rossin; Annette B Steffensen; Moshe Rav Acha; Christopher Newton-Cheh; Arne Pfeufer; Stacey N Lynch; Søren-Peter Olesen; Søren Brunak; Patrick T Ellinor; J Wouter Jukema; Stella Trompet; Ian Ford; Peter W Macfarlane; Bouwe P Krijthe; Albert Hofman; André G Uitterlinden; Bruno H Stricker; Hendrik M Nathoe; Wilko Spiering; Mark J Daly; Folkert W Asselbergs; Pim van der Harst; David J Milan; Paul I W de Bakker; Kasper Lage; Jesper V Olsen
Journal:  Nat Methods       Date:  2014-06-22       Impact factor: 28.547

10.  Unequal evolutionary conservation of human protein interactions in interologous networks.

Authors:  Kevin R Brown; Igor Jurisica
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583
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  194 in total

1.  BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain.

Authors:  Reza Pourhaghighi; Peter E A Ash; Sadhna Phanse; Florian Goebels; Lucas Z M Hu; Siwei Chen; Yingying Zhang; Shayne D Wierbowski; Samantha Boudeau; Mohamed T Moutaoufik; Ramy H Malty; Edyta Malolepsza; Kalliopi Tsafou; Aparna Nathan; Graham Cromar; Hongbo Guo; Ali Al Abdullatif; Daniel J Apicco; Lindsay A Becker; Aaron D Gitler; Stefan M Pulst; Ahmed Youssef; Ryan Hekman; Pierre C Havugimana; Carl A White; Benjamin C Blum; Antonia Ratti; Camron D Bryant; John Parkinson; Kasper Lage; Mohan Babu; Haiyuan Yu; Gary D Bader; Benjamin Wolozin; Andrew Emili
Journal:  Cell Syst       Date:  2020-04-22       Impact factor: 10.304

2.  A Comprehensive Analysis of Nuclear-Encoded Mitochondrial Genes in Schizophrenia.

Authors:  Vanessa F Gonçalves; Carolina Cappi; Christian M Hagen; Adolfo Sequeira; Marquis P Vawter; Andriy Derkach; Clement C Zai; Paula L Hedley; Jonas Bybjerg-Grauholm; Jennie G Pouget; Ari B Cuperfain; Patrick F Sullivan; Michael Christiansen; James L Kennedy; Lei Sun
Journal:  Biol Psychiatry       Date:  2018-03-15       Impact factor: 13.382

3.  PGA: post-GWAS analysis for disease gene identification.

Authors:  Jhih-Rong Lin; Daniel Jaroslawicz; Ying Cai; Quanwei Zhang; Zhen Wang; Zhengdong D Zhang
Journal:  Bioinformatics       Date:  2018-05-15       Impact factor: 6.937

4.  ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97.

Authors:  Bo Wang; Brian A Maxwell; Joung Hyuck Joo; Youngdae Gwon; James Messing; Ashutosh Mishra; Timothy I Shaw; Amber L Ward; Honghu Quan; Sadie Miki Sakurada; Shondra M Pruett-Miller; Tulio Bertorini; Peter Vogel; Hong Joo Kim; Junmin Peng; J Paul Taylor; Mondira Kundu
Journal:  Mol Cell       Date:  2019-04-09       Impact factor: 17.970

5.  A network-based machine-learning framework to identify both functional modules and disease genes.

Authors:  Kuo Yang; Kezhi Lu; Yang Wu; Jian Yu; Baoyan Liu; Yi Zhao; Jianxin Chen; Xuezhong Zhou
Journal:  Hum Genet       Date:  2021-01-07       Impact factor: 4.132

6.  Predicting protein-protein interactions through sequence-based deep learning.

Authors:  Somaye Hashemifar; Behnam Neyshabur; Aly A Khan; Jinbo Xu
Journal:  Bioinformatics       Date:  2018-09-01       Impact factor: 6.937

7.  On entropy and information in gene interaction networks.

Authors:  Z S Wallace; S B Rosenthal; K M Fisch; T Ideker; R Sasik
Journal:  Bioinformatics       Date:  2019-03-01       Impact factor: 6.937

8.  MIPPIE: the mouse integrated protein-protein interaction reference.

Authors:  Gregorio Alanis-Lobato; Jannik S Möllmann; Martin H Schaefer; Miguel A Andrade-Navarro
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

9.  mPPI: a database extension to visualize structural interactome in a one-to-many manner.

Authors:  Yekai Zhou; Hongjun Chen; Sida Li; Ming Chen
Journal:  Database (Oxford)       Date:  2021-06-22       Impact factor: 3.451

10.  Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression.

Authors:  Bing Bai; Xusheng Wang; Yuxin Li; Ping-Chung Chen; Kaiwen Yu; Kaushik Kumar Dey; Jay M Yarbro; Xian Han; Brianna M Lutz; Shuquan Rao; Yun Jiao; Jeffrey M Sifford; Jonghee Han; Minghui Wang; Haiyan Tan; Timothy I Shaw; Ji-Hoon Cho; Suiping Zhou; Hong Wang; Mingming Niu; Ariana Mancieri; Kaitlynn A Messler; Xiaojun Sun; Zhiping Wu; Vishwajeeth Pagala; Anthony A High; Wenjian Bi; Hui Zhang; Hongbo Chi; Vahram Haroutunian; Bin Zhang; Thomas G Beach; Gang Yu; Junmin Peng
Journal:  Neuron       Date:  2020-01-08       Impact factor: 17.173
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