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Protocols

NetPath specifications

Information


Unique identifier OMICS_14109
Name NetPath
Restrictions to use None
Data access File download, Application programming interface
Maintained Yes

Maintainer


  • person_outline Akhilesh Pandey

Publication for NetPath

NetPath citations

 (27)
call_split

Dramatic dysbalancing of the Wnt pathway in breast cancers

2018
Sci Rep
PMCID: 5943245
PMID: 29743726
DOI: 10.1038/s41598-018-25672-6
call_split See protocol

[…] nt signaling (reviewed in,,). The list of 138 validated Wnt target genes was assembled using information provided on website of Nusse laboratory (http://web.stanford.edu/group/nusselab/cgi-bin/wnt/), NetPath and literature. Several Wnt component genes are also well-proven target genes of the pathway, such as FZD, FZD, WNT3A,,.TCGA BRCA patients were separated in two cohorts by their clinically rep […]

library_books

Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

2018
Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] entary Data ): e.g., “TP53 Regulates Transcription of DNA Repair Genes” (Wikipathways), “Notch Signaling Pathway” (Wikipathways), “TP53 Regulates Transcription of DNA Repair Genes” (Reactome), “TCR” (NetPath), “Interleukin-4 and −13 signaling” (Reactome), and “JAK STAT MolecularVariation 2” (INOH). […]

library_books

A Comprehensive View of the β Arrestinome

2017
PMCID: 5337525
PMID: 28321204
DOI: 10.3389/fendo.2017.00032

[…] K293 cells stimulated by angiotensin II, and peptide identification by mass spectrometry (MS) (MudPIT and LC–MS/MS) (). Then, some more β-arrestin partners were sequentially retrieved from queries in NetPath (release 9) (), BioGRID (3.4 version) (), Mentha (25-09-2016 release) (), and HIPPIE (v2.0 24-06-2016) () databases. All the relevant experiments were verified in the original publications. Fi […]

library_books

Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open angle glaucoma

2017
PLoS One
PMCID: 5338784
PMID: 28264060
DOI: 10.1371/journal.pone.0172427

[…] ison between case cohorts (HTG, NTG and all POAG) and all control groups. InnateDB is a publicly available platform incorporating major public domain pathway databases (including KEGG, Reactome, PID, Netpath and INOH). The database contains all human and mouse genes with their associated pathways and interactions. There is also improved annotation of the innate immunity interactome via manual cura […]

library_books

Proteomics in India: the clinical aspect

2016
PMCID: 5097398
PMID: 27822170
DOI: 10.1186/s12014-016-9122-0

[…] high-resolution mass spectrometry, independent drafts of the ‘Human Proteome Maps’ have been published by two investigator led groups which only highlights the biological significance of the data []. NetPath (http://www.netpath.org)—the flagship database of IOB, contains manually curated data for 36 human signaling pathways [–]. Signaling pathways such as Delta-Notch, EGFR1, Hedgehog, TNF-alpha ha […]

library_books

Aberrant DNA methylation in non small cell lung cancer associated fibroblasts

2015
PMCID: 4662832
PMID: 26449251
DOI: 10.1093/carcin/bgv146

[…] h the package KEGGgraph v1.24.0 (). Genes annotated in this pathway were matched to the former list of genes with │Δβ│>0.2. The same procedure was applied to the TGF-β receptor signaling pathway from Netpath database (NetPath_7) (). Complete package references and further details are provided in Supplementary Material, available at Carcinogenesis Online. […]

Citations

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NetPath institution(s)
Institute of Bioinformatics, International Tech Park, Bangalore, India; McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA; Research Unit for Immunoinformatics, RIKEN Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Kanagawa, Japan; Department of Biotechnology and Bioinformatics, Kuvempu University, Jnanasahyadri, Shimoga, India; Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA; Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Department of Molecular Biology and Genetics, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Ludwig Institute for Cancer Research, Brussels Branch, and the Experimental Medicine Unit, Christian de Duve Institute of Cellular Pathology, Universite Catholique de Louvain, Brussels, Belgium; Laboratory for Immunogenomics, RIKEN Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Kanagawa, Japan; Department of Human Genome Technology, Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba, Japan; Laboratory for Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa, Japan; Laboratories of Developmental Immunology, Graduate School of Frontier Biosciences and Graduate School of Medicine, Osaka University, Osaka, Japan; Research Institute for Biological Sciences, Tokyo University of Science, Yamazaki, Noda City, Chiba, Japan; Signal/Network Team, RIKEN Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi, Yokohama, Kanagawa, Japan; IMGENEX India Pvt. Ltd., Bhubaneswar, Orissa, India; Department of Computer Science, Wayne State University, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA; Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
NetPath funding source(s)
This work was supported by the Johns Hopkins Breast Cancer SPORE (grant n°CA 88843) Career Development Award, the Department of Defense Era of Hope Scholar (grant n°W81XWH-06-1-0428) and the National Institutes of Health (grant n°U54 RR020839).

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