NetPath

NetPath[1] is a manually curated resource of human

NetPath
signal transduction pathways. It is a joint effort
between Pandey Lab at the Johns Hopkins University
and the Institute of Bioinformatics (IOB), Bangalore,
India,[2] and is also worked on by other parties.

NetPath hosts 45 signaling pathways, including 10

pathways with a major role in the regulation of immune
system and 10 pathways with relevance to regulation of
cancer.

Overview Content
Description curated signal transduction
The 45 pathways contain information pertaining to pathways.
protein-protein interactions, enzyme-protein substrate
reactions which bring about post translational Contact
modifications (PTMs) and also a catalogue of genes Laboratory Institute of Bioinformatics,
which are differentially regulated upon activation of Bangalore
specific ligand mediated receptor pathways. The [1]
molecules which localises to different cellular Primary citation Kandasamy & al. (2010)
organelles due to their PTMs or specific protein-protein Release date 2010
interactions which occur downstream of ligand- Access
receptor mediated pathway are available under
translocation events. Recently, NetPath has also curated Website http://www.netpath.org
the molecules involved in the transcriptional regulation
of genes in the context of immune signaling pathways. The reactions in NetPath are curated by PhD level
scientists from experimental evidence available in published research articles. NetPath also contains textual
description of its reactions with information on PTMs, dependence of PTMs on various signaling reactions,
subcellular location, protein interaction domains or motifs and the cell type or cell line in which reactions
are proved. The information in NetPath is linked to their corresponding research articles and are frequently
updated. Each pathway is subjected to different level of internal quality checks and peer-review by the
pathway experts and authorities.

Development
NetPath was developed using PathBuilder, an open source software application for annotating and
developing pathway resources.[3] PathBuilder enables annotation of molecular events including protein-
protein interactions, enzyme-substrate relationships and protein translocation events via manual or
automatic methods. The features of PathBuilder include automatic validation of data formats, built-in
modules for visualizing pathways, automated import of data from other pathway resources, export of data
in several standard data exchange formats and an application programming interface for retrieving pathway
datasets.

Data availability
All 45 pathways are freely downloadable in BioPAX, PSI-MI and SBML formats. BioPAX is an emerging
standard for pathway data exchange. The pathways are made available under an adaptive Creative
Commons License 2.5 which stipulates that the pathways may be used if adequate credit is given to the
authors.

Immune signaling pathways

The following immune signaling pathways are hosted by Netpath:

B cell receptor pathway[4]

T cell receptor pathway[5]
Interleukin-1 pathway[6]
Interleukin-2 pathway[7]
Interleukin-3 pathway[8]
Interleukin-4 pathway[9]
Interleukin-5 pathway[10]
Interleukin-6 pathway[11]
Interleukin-7 pathway[12]
Interleukin-9 pathway[13]

Cancer signaling pathways

The cancer signaling pathways were developed in collaboration with the Computational Biology Center at
Memorial Sloan–Kettering Cancer Center and with Bader Lab at the University of Toronto for the "Cancer
Cell Map". The following cancer signaling pathways are hosted by Netpath:

Epidermal growth factor receptor Pathway[14]

Transforming growth factor beta receptor pathway[15]
Tumor necrosis factor alpha pathway[16]
Alpha6 Beta4 Integrin pathway[17]
Inhibitor of DNA binding pathway[18]
Hedgehog pathway[19]
Notch pathway[20]
Wnt pathway[21]
Androgen receptor pathway[22]
 Kit receptor pathway[23]

Current statistics
Curated pathways 45

Molecules involved 1,053

Physical interactions 2,448

Genes transcriptionally regulated 7,401

Transport 284
Enzyme catalysis 1,597

PubMed citations 2,228

Community participation programme

The community participation programme is aimed at training the students in various universities from India
on curation of pathway reactions. This is a joint programme led by the Institute of Bioinformatics (IOB),
Bangalore, India with active participation from Akhilesh Pandey's laboratory at the Johns Hopkins
University (USA) and Gary Bader's lab at the University of Toronto, Canada. Currently, students from 3
major Indian Universities namely Pondicherry University, University of Pune and University of Mysore are
participants of this community effort.

References
1. Kandasamy, Kumaran; Mohan, Sujatha; Raju, Rajesh; Keerthikumar, Shivakumar; Kumar,
Ghantasala S Sameer; Venugopal, Abhilash K; Telikicherla, Deepthi; Navarro, Daniel J;
Mathivanan, Suresh (2010). "NetPath: a public resource of curated signal transduction
pathways" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847715). Genome Biology. 11
(1): R3. doi:10.1186/gb-2010-11-1-r3 (https://doi.org/10.1186%2Fgb-2010-11-1-r3).
PMC 2847715 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847715). PMID 20067622
(https://pubmed.ncbi.nlm.nih.gov/20067622).
2. Dr. Akhilesh Pandey's laboratory (http://pandeylab.igm.jhmi.edu)
3. Kandasamy, K.; Keerthikumar, S.; Raju, R.; Keshava Prasad, T. S.; Ramachandra, Y. L.;
Mohan, S.; Pandey, A. (2009). "PathBuilder--open source software for annotating and
developing pathway resources" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781757).
Bioinformatics. 25 (21): 2860–2. doi:10.1093/bioinformatics/btp453 (https://doi.org/10.1093%
2Fbioinformatics%2Fbtp453). PMC 2781757 (https://www.ncbi.nlm.nih.gov/pmc/articles/PM
C2781757). PMID 19628504 (https://pubmed.ncbi.nlm.nih.gov/19628504).
4. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_12).
5. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_11).
6. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_13).
7. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_14).
 8. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_15).
9. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_16).
10. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_17).
11. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_18).
12. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_19).
13. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_20).
14. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_4).
15. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_7).
16. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_9).
17. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_1).
18. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_5).
19. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_10).
20. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_3).
21. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_8).
22. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_2).
23. "NetPath - Signal Transduction Pathways" (http://www.netpath.org/pathways?path_id=NetP
ath_6).

External links
NetPath (https://web.archive.org/web/20120920084537/http://www.netpath.org/)

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