How to cite iPTMnet and its sources
If you use iPTMnet please include this citation:
Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH. iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res. 2018 Jan 4;46(D1):D542-D550. doi: 10.1093/nar/gkx1104. PMID: 29145615; PMCID: PMC5753337.
Citations of the underlying Sources
| # | Name | Publication | PubMed |
|---|---|---|---|
| 1 | HPRD | Prasad, T. S. K. et al. (2009) Human Protein Reference Database - 2009 Update. Nucleic Acids Research. 37, D767-72. | 18988627 |
| 2 | phospho.ELM | Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Nucleic Acids Res. 2011 Jan;39(Database issue) 261-7. doi: 10.1093/nar/gkq1104. | 21062810 |
| 3 | p3DB | Yao Q, Ge H, Wu S, Zhang N, Chen W, Xu C, Gao J, Thelen JJ, Xu D. (2013) P3DB 3.0: From plant phosphorylation sites to protein networks. Nucleic Acids Res 2013. 42(Database issue):D1206-D1213 | 24243849 |
| 4 | BioGRID | Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. 2006; 34:D535-9. | 16381927 |
| Oughtred R, Stark C, Breitkreutz BJ, Reguly T, Boucher L, Chang C, Kolas N, O'Donnell L, Leung G, McAdam R, Zhang F, Dolma S, Willems A, Coulombe-Huntington J, Chatr-Aryamontri A, Dolinski K, Tyers M. The BioGRID interaction database: 2019 update.Nucleic Acids Res. 2019; 47:D529-41. | 30476227 | ||
| Sadowski I, Breitkreutz BJ, Stark C, Su T-C, Dahabieh M, Raithatha S, Bernhard W, Oughtred R, Dolinski K, Barreto K, Myers M. The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. Database. 2013:bat026. | 23674503 | ||
| 5 | PomBase | Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG. PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res. 2012;40(Database issue):D695-9. Epub 2011 | 22039153 |
| 6 | neXtProt | Gaudet P, Michel PA, Zahn-Zabal M, Britan A, Cusin I, Domagalski M, Duek PD, Gateau A, Gleizes A, Hinard V, Rech de Laval V, Lin JJ, Nikitin F, Schaeffer M, Teixeira D, Lane L, Bairoch A. The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res. 2017; 45(D1):D177-D182 doi:10.1093/nar/gkw1062 | 27899619 |
| 7 | Signor | Perfetto L, Briganti L, Calderone A, Cerquone Perpetuini A, Iannuccelli M, Langone F, Licata L, Marinkovic M, Mattioni A, Pavlidou T, Peluso D, Petrilli LL, Pirrò S, Posca D, Santonico E, Silvestri A, Spada F, Castagnoli L, Cesareni G. SIGNOR: a database of causal relationships between biological entities. Nucleic Acids Res. 2016;44(D1):D548-54. doi: 10.1093/nar/gkv1048 | 26467481 |
| 8 | dbSNO | Chen YJ, Lu CT, Su MG, Huang KY, Ching WC, Yang HH, Liao YC, Chen YJ, Lee TY. dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. Nucleic Acids Res. 2015;43(Database issue):D503-11. doi: 10.1093/nar/gku1176. | 25399423 |
| 9 | PhosphoSitePlus | Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015;43(Database issue):D512-20. doi: 10.1093/nar/gku1267. | 25514926 |
| 10 | PhosPhAt | Durek P, Schmidt R, Heazlewood JL, Jones A, Maclean D, Nagel A, Kersten B, Schulze WX. PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res. 38: D828-D834 (2010) | 17984086 |
| 11 | UniProt | The UniProt Consortium. UniProt: the universal protein knowledgebase Nucleic Acids Res. 45: D158-D169 (2017) | 27899622 |
| 12 | PRO | Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K,Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res.2017;45(D1):D339-D346. doi: 10.1093/nar/gkw1075. | 27899649 |
| 13 | RLIMS-P | Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huang H, Vijay-Shanker K, Wu CH. RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. Database (Oxford).2014. pii: bau081. doi: 10.1093/database/bau081. | 25122463 |
| 14 | eFIP | Wang Q, Ross KE, Huang H, Ren J, Li G, Vijay-Shanker K, Wu CH, Arighi CN. Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature. Methods Mol Biol. 2017;1558:213-232. doi: 10.1007/978-1-4939-6783-4_10. | 28150240 |
| 15 | SGD | Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM. Curated protein information in the Saccharomyces genome database. Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax011 | 28365727 |
| 16 | Biomuta | Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancerbiomarker discovery. Nucleic Acids Res. 2018 Jan 4;46(D1):D1128-D1136. doi:10.1093/nar/gkx907 | 30053270 |
| 17 | IntAct | Orchard S, Ammari M, Aranda B, et al. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Research. 2014 Jan;42(Database issue):D358-63. DOI: 10.1093/nar/gkt1115. | 24234451 |
| 18 | GlyGen | York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings, RD, Feizi T, Martin M, et al. GlyGen: computational and informatics resources for glycoscience. Glycobiology. 2020. 30(2), 72-73. | 31616925 |
| 19 | IEDB | Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky1006. | 30357391 |
