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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.
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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
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NetPath was developed using PathBuilder, an open source software application for annotating and developing pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events via manual or
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due to their PTMs or specific protein-protein interactions which occur downstream of ligand-receptor mediated pathway are available under translocation events. Recently, NetPath has also curated the molecules involved in the
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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
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Kandasamy, Kumaran; Mohan, Sujatha; Raju, Rajesh; Keerthikumar, Shivakumar; Kumar, Ghantasala S Sameer; Venugopal, Abhilash K; Telikicherla, Deepthi; Navarro, Daniel J; Mathivanan, Suresh (2010).
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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
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formats. BioPAX is an emerging standard for pathway data exchange. The pathways are made available under an adaptive
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Kandasamy, K.; Keerthikumar, S.; Raju, R.; Keshava Prasad, T. S.; Ramachandra, Y. L.; Mohan, S.; Pandey, A. (2009).
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The cancer signaling pathways were developed in collaboration with the
Computational Biology Center at
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148:(PTMs) and also a catalogue of genes which are differentially regulated upon activation of specific
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NetPath hosts 45 signaling pathways, including 10 pathways with a major role in the regulation of
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which stipulates that the pathways may be used if adequate credit is given to the authors.
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for the "Cancer Cell Map". The following cancer signaling pathways are hosted by
Netpath:
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515:"PathBuilder--open source software for annotating and developing pathway resources"
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419:, Canada. Currently, students from 3 major Indian Universities namely
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453:"NetPath: a public resource of curated signal transduction pathways"
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The following immune signaling pathways are hosted by
Netpath:
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signaling reactions, subcellular location, protein interaction
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pathways. The molecules which localises to different cellular
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pathways. It is a joint effort between Pandey Lab at the
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144:, enzyme-protein substrate reactions which bring about
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140:The 45 pathways contain information pertaining to
283:Transforming growth factor beta receptor pathway
128:and 10 pathways with relevance to regulation of
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431:are participants of this community effort.
204:All 45 pathways are freely downloadable in
121:, and is also worked on by other parties.
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829:"NetPath - Signal Transduction Pathways"
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801:"NetPath - Signal Transduction Pathways"
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661:"NetPath - Signal Transduction Pathways"
647:"NetPath - Signal Transduction Pathways"
633:"NetPath - Signal Transduction Pathways"
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605:"NetPath - Signal Transduction Pathways"
591:"NetPath - Signal Transduction Pathways"
577:"NetPath - Signal Transduction Pathways"
563:"NetPath - Signal Transduction Pathways"
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280:Epidermal growth factor receptor Pathway
187:by the pathway experts and authorities.
105:is a manually curated resource of human
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266:Memorial Sloan–Kettering Cancer Center
64:Institute of Bioinformatics, Bangalore
50:curated signal transduction pathways.
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286:Tumor necrosis factor alpha pathway
415:(USA) and Gary Bader's lab at the
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391:Community participation programme
350:Genes transcriptionally regulated
502:Dr. Akhilesh Pandey's laboratory
407:with active participation from
292:Inhibitor of DNA binding pathway
146:post translational modifications
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1:
531:10.1093/bioinformatics/btp453
289:Alpha6 Beta4 Integrin pathway
214:Creative Commons License 2.5
142:protein-protein interactions
397:Institute of Bioinformatics
115:Institute of Bioinformatics
73:Kandasamy & al. (2010)
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163:transcriptional regulation
304:Androgen receptor pathway
260:Cancer signaling pathways
220:Immune signaling pathways
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866:Johns Hopkins University
413:Johns Hopkins University
111:Johns Hopkins University
470:10.1186/gb-2010-11-1-r3
231:T cell receptor pathway
228:B cell receptor pathway
421:Pondicherry University
95:http://www.netpath.org
417:University of Toronto
411:'s laboratory at the
340:Physical interactions
274:University of Toronto
255:Interleukin-9 pathway
252:Interleukin-7 pathway
249:Interleukin-6 pathway
246:Interleukin-5 pathway
243:Interleukin-4 pathway
240:Interleukin-3 pathway
237:Interleukin-2 pathway
234:Interleukin-1 pathway
861:Biological databases
429:University of Mysore
307:Kit receptor pathway
871:2010 establishments
107:signal transduction
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425:University of Pune
330:Molecules involved
312:Current statistics
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200:Data availability
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119:Bangalore, India
70:Primary citation
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78:Release date
301:Wnt pathway
191:Development
185:peer-review
47:Description
855:Categories
435:References
158:organelles
60:Laboratory
463:(1): R3.
401:Bangalore
360:Transport
270:Bader Lab
268:and with
180:cell line
176:cell type
152:mediated
549:19628504
489:20067622
174:and the
154:receptor
136:Overview
113:and the
846:NetPath
540:2781757
480:2847715
399:(IOB),
272:at the
168:domains
117:(IOB),
103:NetPath
91:Website
55:Contact
42:Content
28:NetPath
18:Netpath
547:
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384:2,228
374:1,597
354:7,401
344:2,448
334:1,053
206:BioPAX
172:motifs
150:ligand
130:cancer
86:Access
405:India
545:PMID
485:PMID
427:and
364:284
210:SBML
81:2010
535:PMC
527:doi
475:PMC
465:doi
324:45
178:or
170:or
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
