NetPath: a Public Resource of Curated Signal Transduction Pathways

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.

Citing Articles

Dysregulated Pathways During Pregnancy Predict Drug Candidates in Neurodevelopmental Disorders.

Yin H, Wang Z, Wang W, Liu J, Xue Y, Liu L Neurosci Bull. 2025; .

PMID: 39913063 DOI: 10.1007/s12264-025-01360-0.

Automatic construction of Petri net models for computational simulations of molecular interaction network.

Lin X, Chang X, Zhang Y, Gao Z, Chi X NPJ Syst Biol Appl. 2024; 10(1):131.

PMID: 39521772 PMC: 11550427. DOI: 10.1038/s41540-024-00464-z.

HNCDrugResDb: a platform for deciphering drug resistance in head and neck cancers.

Palollathil A, Nandakumar R, Ahmed M, Velikkakath A, Nisar M, Nisar M Sci Rep. 2024; 14(1):25327.

PMID: 39455682 PMC: 11511878. DOI: 10.1038/s41598-024-75861-9.

Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction.

Arici M, Tuncbag N Brief Bioinform. 2024; 25(5).

PMID: 39163205 PMC: 11334722. DOI: 10.1093/bib/bbae399.

DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning.

Huang Y, Dong D, Zhang W, Wang R, Lin Y, Zuo H Database (Oxford). 2024; 2024.

PMID: 38994794 PMC: 11240114. DOI: 10.1093/database/baae051.

References

Joshi-Tope G, Gillespie M, Vastrik I, DEustachio P, Schmidt E, de Bono B . Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2004; 33(Database issue):D428-32. PMC: 540026. DOI: 10.1093/nar/gki072. View

Keshava Prasad T, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S . Human Protein Reference Database--2009 update. Nucleic Acids Res. 2008; 37(Database issue):D767-72. PMC: 2686490. DOI: 10.1093/nar/gkn892. View

Pico A, Kelder T, van Iersel M, Hanspers K, Conklin B, Evelo C . WikiPathways: pathway editing for the people. PLoS Biol. 2008; 6(7):e184. PMC: 2475545. DOI: 10.1371/journal.pbio.0060184. View

Grimm E, Mazumder A, Zhang H, Rosenberg S . Lymphokine-activated killer cell phenomenon. Lysis of natural killer-resistant fresh solid tumor cells by interleukin 2-activated autologous human peripheral blood lymphocytes. J Exp Med. 1982; 155(6):1823-41. PMC: 2186695. DOI: 10.1084/jem.155.6.1823. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

Nakamura M, Asao H, Takeshita T, Sugamura K . Interleukin-2 receptor heterotrimer complex and intracellular signaling. Semin Immunol. 1993; 5(5):309-17. DOI: 10.1006/smim.1993.1037. View

Hoffmann R, Valencia A . A gene network for navigating the literature. Nat Genet. 2004; 36(7):664. DOI: 10.1038/ng0704-664. View

Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R . PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics. 2002; 18(7):996-1003. DOI: 10.1093/bioinformatics/18.7.996. View

Barrett T, Troup D, Wilhite S, Ledoux P, Rudnev D, Evangelista C . NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res. 2006; 35(Database issue):D760-5. PMC: 1669752. DOI: 10.1093/nar/gkl887. View

10.

Rosenberg S . Progress in human tumour immunology and immunotherapy. Nature. 2001; 411(6835):380-4. DOI: 10.1038/35077246. View

11.

Paredes R, Lopez Benaldo de Quiros J, Fernandez-Cruz E, Clotet B, Lane H . The potential role of interleukin-2 in patients with HIV infection. AIDS Rev. 2002; 4(1):36-40. View

12.

Noguchi M, Yi H, Rosenblatt H, Filipovich A, Adelstein S, Modi W . Interleukin-2 receptor gamma chain mutation results in X-linked severe combined immunodeficiency in humans. Cell. 1993; 73(1):147-57. DOI: 10.1016/0092-8674(93)90167-o. View

13.

Draghici S, Khatri P, Tarca A, Amin K, Done A, Voichita C . A systems biology approach for pathway level analysis. Genome Res. 2007; 17(10):1537-45. PMC: 1987343. DOI: 10.1101/gr.6202607. View

14.

Schaefer C . Pathway databases. Ann N Y Acad Sci. 2004; 1020:77-91. DOI: 10.1196/annals.1310.009. View

15.

Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B . Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res. 2008; 37(Database issue):D773-81. PMC: 2686511. DOI: 10.1093/nar/gkn701. View

16.

Kim H, Imbert J, Leonard W . Both integrated and differential regulation of components of the IL-2/IL-2 receptor system. Cytokine Growth Factor Rev. 2006; 17(5):349-66. DOI: 10.1016/j.cytogfr.2006.07.003. View

17.

Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad T, Ramachandra Y, Mohan S . PathBuilder--open source software for annotating and developing pathway resources. Bioinformatics. 2009; 25(21):2860-2. PMC: 2781757. DOI: 10.1093/bioinformatics/btp453. View

18.

Ellery J, Nicholls P . Alternate signalling pathways from the interleukin-2 receptor. Cytokine Growth Factor Rev. 2001; 13(1):27-40. DOI: 10.1016/s1359-6101(01)00023-5. View

19.

Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M . pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res. 2005; 34(Database issue):D527-34. PMC: 1347407. DOI: 10.1093/nar/gkj044. View

20.

Lin J, Leonard W . Signaling from the IL-2 receptor to the nucleus. Cytokine Growth Factor Rev. 1998; 8(4):313-32. DOI: 10.1016/s1359-6101(97)00021-x. View