Literature DB >> 19079255

Integrated network analysis platform for protein-protein interactions.

Jianmin Wu1, Tea Vallenius, Kristian Ovaska, Jukka Westermarck, Tomi P Mäkelä, Sampsa Hautaniemi.   

Abstract

There is an increasing demand for network analysis of protein-protein interactions (PPIs). We introduce a web-based protein interaction network analysis platform (PINA), which integrates PPI data from six databases and provides network construction, filtering, analysis and visualization tools. We demonstrated the advantages of PINA by analyzing two human PPI networks; our results suggested a link between LKB1 and TGFbeta signaling, and revealed possible competitive interactors of p53 and c-Jun.

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Year:  2008        PMID： 19079255     DOI： 10.1038/nmeth.1282

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


  20 in total

Review 1.  Interactome: gateway into systems biology.

Authors:  Michael E Cusick; Niels Klitgord; Marc Vidal; David E Hill
Journal:  Hum Mol Genet       Date:  2005-09-14       Impact factor: 6.150

2.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

Review 3.  The LKB1 tumor suppressor kinase in human disease.

Authors:  Pekka Katajisto; Tea Vallenius; Kari Vaahtomeri; Niklas Ekman; Lina Udd; Marianne Tiainen; Tomi P Mäkelä
Journal:  Biochim Biophys Acta       Date:  2006-08-16

4.  C-TAK1 protein kinase phosphorylates human Cdc25C on serine 216 and promotes 14-3-3 protein binding.

Authors:  C Y Peng; P R Graves; S Ogg; R S Thoma; M J Byrnes; Z Wu; M T Stephenson; H Piwnica-Worms
Journal:  Cell Growth Differ       Date:  1998-03

5.  Human SAD1 kinase is involved in UV-induced DNA damage checkpoint function.

Authors:  Rui Lu; Hiroyuki Niida; Makoto Nakanishi
Journal:  J Biol Chem       Date:  2004-05-18       Impact factor: 5.157

6.  LKB1 signaling in mesenchymal cells required for suppression of gastrointestinal polyposis.

Authors:  Pekka Katajisto; Kari Vaahtomeri; Niklas Ekman; Eeva Ventelä; Ari Ristimäki; Nabeel Bardeesy; Robert Feil; Ronald A DePinho; Tomi P Mäkelä
Journal:  Nat Genet       Date:  2008-03-02       Impact factor: 38.330

7.  Development of human protein reference database as an initial platform for approaching systems biology in humans.

Authors:  Suraj Peri; J Daniel Navarro; Ramars Amanchy; Troels Z Kristiansen; Chandra Kiran Jonnalagadda; Vineeth Surendranath; Vidya Niranjan; Babylakshmi Muthusamy; T K B Gandhi; Mads Gronborg; Nieves Ibarrola; Nandan Deshpande; K Shanker; H N Shivashankar; B P Rashmi; M A Ramya; Zhixing Zhao; K N Chandrika; N Padma; H C Harsha; A J Yatish; M P Kavitha; Minal Menezes; Dipanwita Roy Choudhury; Shubha Suresh; Neelanjana Ghosh; R Saravana; Sreenath Chandran; Subhalakshmi Krishna; Mary Joy; Sanjeev K Anand; V Madavan; Ansamma Joseph; Guang W Wong; William P Schiemann; Stefan N Constantinescu; Lily Huang; Roya Khosravi-Far; Hanno Steen; Muneesh Tewari; Saghi Ghaffari; Gerard C Blobe; Chi V Dang; Joe G N Garcia; Jonathan Pevsner; Ole N Jensen; Peter Roepstorff; Krishna S Deshpande; Arul M Chinnaiyan; Ada Hamosh; Aravinda Chakravarti; Akhilesh Pandey
Journal:  Genome Res       Date:  2003-10       Impact factor: 9.043

8.  The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Authors:  Henning Hermjakob; Luisa Montecchi-Palazzi; Gary Bader; Jérôme Wojcik; Lukasz Salwinski; Arnaud Ceol; Susan Moore; Sandra Orchard; Ugis Sarkans; Christian von Mering; Bernd Roechert; Sylvain Poux; Eva Jung; Henning Mersch; Paul Kersey; Michael Lappe; Yixue Li; Rong Zeng; Debashis Rana; Macha Nikolski; Holger Husi; Christine Brun; K Shanker; Seth G N Grant; Chris Sander; Peer Bork; Weimin Zhu; Akhilesh Pandey; Alvis Brazma; Bernard Jacq; Marc Vidal; David Sherman; Pierre Legrain; Gianni Cesareni; Ioannis Xenarios; David Eisenberg; Boris Steipe; Chris Hogue; Rolf Apweiler
Journal:  Nat Biotechnol       Date:  2004-02       Impact factor: 54.908

9.  IntAct--open source resource for molecular interaction data.

Authors:  S Kerrien; Y Alam-Faruque; B Aranda; I Bancarz; A Bridge; C Derow; E Dimmer; M Feuermann; A Friedrichsen; R Huntley; C Kohler; J Khadake; C Leroy; A Liban; C Lieftink; L Montecchi-Palazzi; S Orchard; J Risse; K Robbe; B Roechert; D Thorneycroft; Y Zhang; R Apweiler; H Hermjakob
Journal:  Nucleic Acids Res       Date:  2006-12-01       Impact factor: 16.971

10.  The BioGRID Interaction Database: 2008 update.

Authors:  Bobby-Joe Breitkreutz; Chris Stark; Teresa Reguly; Lorrie Boucher; Ashton Breitkreutz; Michael Livstone; Rose Oughtred; Daniel H Lackner; Jürg Bähler; Valerie Wood; Kara Dolinski; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2007-11-13       Impact factor: 16.971
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  141 in total

1.  The Sharpin interactome reveals a role for Sharpin in lamellipodium formation via the Arp2/3 complex.

Authors:  Meraj H Khan; Siiri I Salomaa; Guillaume Jacquemet; Umar Butt; Mitro Miihkinen; Takahiro Deguchi; Elena Kremneva; Pekka Lappalainen; Martin J Humphries; Jeroen Pouwels
Journal:  J Cell Sci       Date:  2017-08-03       Impact factor: 5.285

Review 2.  Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry.

Authors:  Robyn M Kaake; Xiaorong Wang; Lan Huang
Journal:  Mol Cell Proteomics       Date:  2010-05-05       Impact factor: 5.911

3.  dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.

Authors:  Peilin Jia; Siyuan Zheng; Jirong Long; Wei Zheng; Zhongming Zhao
Journal:  Bioinformatics       Date:  2010-11-02       Impact factor: 6.937

4.  ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations.

Authors:  Emile R Chimusa; Mamana Mbiyavanga; Gaston K Mazandu; Nicola J Mulder
Journal:  Bioinformatics       Date:  2015-10-27       Impact factor: 6.937

5.  Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.

Authors:  Yuba Raj Pokharel; Jani Saarela; Agnieszka Szwajda; Christian Rupp; Anne Rokka; Shibendra Lal Kumar Karna; Kaisa Teittinen; Garry Corthals; Olli Kallioniemi; Krister Wennerberg; Tero Aittokallio; Jukka Westermarck
Journal:  Mol Cell Proteomics       Date:  2015-10-23       Impact factor: 5.911

Review 6.  Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives.

Authors:  Peilin Jia; Zhongming Zhao
Journal:  Hum Genet       Date:  2014-02       Impact factor: 4.132

7.  Integrating GWASs and human protein interaction networks identifies a gene subnetwork underlying alcohol dependence.

Authors:  Shizhong Han; Bao-Zhu Yang; Henry R Kranzler; Xiaoming Liu; Hongyu Zhao; Lindsay A Farrer; Eric Boerwinkle; James B Potash; Joel Gelernter
Journal:  Am J Hum Genet       Date:  2013-11-21       Impact factor: 11.025

8.  Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.

Authors:  Ben C Collins; Ludovic C Gillet; George Rosenberger; Hannes L Röst; Anton Vichalkovski; Matthias Gstaiger; Ruedi Aebersold
Journal:  Nat Methods       Date:  2013-10-27       Impact factor: 28.547

9.  Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery.

Authors:  Felicia Walton Pagliuca; Mark O Collins; Agata Lichawska; Philip Zegerman; Jyoti S Choudhary; Jonathon Pines
Journal:  Mol Cell       Date:  2011-08-05       Impact factor: 17.970

10.  Virus interactions with human signal transduction pathways.

Authors:  Zhongming Zhao; Junfeng Xia; Oznur Tastan; Irtisha Singh; Meghana Kshirsagar; Jaime Carbonell; Judith Klein-Seetharaman
Journal:  Int J Comput Biol Drug Des       Date:  2011-02-17
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