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NetPath: a public resource of curated signal transduction pathways

Kumaran Kandasamy1,2†, S Sujatha Mohan1,3†, Rajesh Raju1,4, Shivakumar Keerthikumar1, Ghantasala SS Kumar1, Abhilash K Venugopal1, Deepthi Telikicherla1, J Daniel Navarro1, Suresh Mathivanan1, Christian Pecquet3, Sashi K Gollapudi1, Sudhir G Tattikota1, Shyam Mohan1, Hariprasad Padhukasahasram1, Yashwanth Subbannayya1, Renu Goel1, Harrys KC Jacob1,2, Jun Zhong2, Raja Sekhar1, Vishalakshi Nanjappa1, Lavanya Balakrishnan1, Roopashree Subbaiah1, YL Ramachandra4, B Abdul Rahiman4, TS Keshava Prasad1, Jian-Xin Lin5, Jon CD Houtman6, Stephen Desiderio7, Jean-Christophe Renauld8, Stefan N Constantinescu8, Osamu Ohara10,9, Toshio Hirano11,12, Masato Kubo13,14, Sujay Singh15, Purvesh Khatri16, Sorin Draghici16,17, Gary D Bader18,19, Chris Sander19, Warren J Leonard5 and Akhilesh Pandey2,20*

  • * Corresponding author: Akhilesh Pandey pandey@jhmi.edu

  • † Equal contributors

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Author affiliations

1 Institute of Bioinformatics, International Tech Park, Bangalore 560066, India

2 McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA

3 Current address: Research Unit for Immunoinformatics, RIKEN Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Kanagawa 230-0045, Japan

4 Department of Biotechnology and Bioinformatics, Kuvempu University, Jnanasahyadri, Shimoga 577451, India

5 Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA

6 Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA

7 Department of Molecular Biology and Genetics, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA

8 The Ludwig Institute for Cancer Research, Brussels Branch, and the Experimental Medicine Unit, Christian de Duve Institute of Cellular Pathology, Universite Catholique de Louvain, avenue Hippocrate 74, B-1200-Brussels, Belgium

9 Laboratory for Immunogenomics, RIKEN Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Kanagawa 230-0045, Japan

10 Department of Human Genome Technology, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan

11 Laboratory for Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan

12 Laboratories of Developmental Immunology, Graduate School of Frontier Biosciences and Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan

13 Research Institute for Biological Sciences, Tokyo University of Science, Yamazaki, Noda City, Chiba 278-0022, Japan

14 Signal/Network Team, RIKEN Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan

15 IMGENEX India Pvt. Ltd., Bhubaneswar, Orissa 92121, India

16 Department of Computer Science, Wayne State University, Detroit, Michigan 48202, USA

17 Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48202, USA

18 Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada

19 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA

20 Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21205, USA

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Citation and License

Genome Biology 2010, 11:R3 doi:10.1186/gb-2010-11-1-r3

Published: 12 January 2010

Abstract

We have developed NetPath as a resource of curated human signaling pathways. As an initial step, NetPath provides detailed maps of a number of immune signaling pathways, which include approximately 1,600 reactions annotated from the literature and more than 2,800 instances of transcriptionally regulated genes - all linked to over 5,500 published articles. We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches.