The neXtProt knowledgebase on human proteins: 2017 update

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D177-D182

  Gaudet, Pascale ^a,b   Michel, Pierre André ^a   Zahn Zabal, Monique ^a   Britan, Aurore ^a   Cusin, Isabelle ^a   Domagalski, Marcin ^a,b   Duek, Paula D ^a   Gateau, Alain ^a   Gleizes, Anne ^a   Hinard, Valérie ^a   De Laval, Valentine Rech ^a,b   Lin, JinJin ^c   Nikitin, Frederic ^a   Schaeffer, Mathieu ^a,b   Teixeira, Daniel ^a   Lane, Lydie ^a,b   Bairoch, Amos ^a,b  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHANNELOPATHY; GENETIC VARIATION; HEREDITARY TUMOR; KNOWLEDGE BASE; MASS SPECTROMETRY; ONTOLOGY; PHENOTYPIC VARIATION; PROTEIN DATABASE; PROTEIN PROCESSING; PROTEOMICS; GENETIC ASSOCIATION STUDY; HUMAN; INTERNET; PHENOTYPE; PROCEDURES; SOFTWARE; WEB BROWSER;

DATABASES, PROTEIN; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; HUMANS; INTERNET; PHENOTYPE; PROTEOMICS; SOFTWARE; WEB BROWSER;

EID: 85016095124     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1062     Document Type: Article

References (25)

1. Gaudet, P., Michel, P.A., Zahn-Zabal, M., Cusin, I., Duek, P.D., Evalet, O., Gateau, A., Gleizes, A., Pereira, M., Teixeira, D. et al. (2015) The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res., 43, D764-D770.
2. Gaudet, P., Argoud-Puy, G., Cusin, I., Duek, P., Evalet, O., Gateau, A., Gleizes, A., Pereira, M., Zahn-Zabal, M., Zwahlen, C. et al. (2013) neXtProt: organizing protein knowledge in the context of human proteome projects. J. Proteome Res., 12, 293-298.
3. Lane, L., Argoud-Puy, G., Britan, A., Cusin, I., Duek, P.D., Evalet, O., Gateau, A., Gaudet, P., Gleizes, A., Masselot, A. et al. (2012) neXtProt: a knowledge platform for human proteins. Nucleic Acids Res., 40, D76-D83.
4. Breuza, L., Poux, S., Estreicher, A., Famiglietti, M.L., Magrane, M., Tognolli, M., Bridge, A., Baratin, D. and Redaschi, N. (2016) The UniProtKB guide to the human proteome. Database (Oxford), 2016, bav120.
5. Rosikiewicz, M., Comte, A., Niknejad, A., Robinson-Rechavi, M. and Bastian, F.B. (2013) Uncovering hidden duplicated content in public transcriptomics data. Database (Oxford), 2013, bat010.
6. Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S. et al. (2010) Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol., 28, 1248-1250.
7. Farrah, T., Deutsch, E.W., Omenn, G.S., Sun, Z., Watts, J.D., Yamamoto, T., Shteynberg, D., Harris, M.M. and Moritz, R.L. (2014) State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biologyand disease-driven human proteome project. J. Proteome Res., 13, 60-75.
8. Kusebauch, U., Campbell, D.S., Deutsch, E.W., Chu, C.S., Spicer, D.A., Brusniak, M.Y., Slagel, J., Sun, Z., Stevens, J., Grimes, B. et al. (2016) Human SRMAtlas: A resource of targeted assays to quantify the complete human proteome. Cell, 166, 766-778.
9. Huntley, R.P., Sawford, T., Mutowo-Meullenet, P., Shypitsyna, A., Bonilla, C., Martin, M.J. and O'Donovan, C. (2015) The GOA database: gene ontology annotation updates for 2015. Nucleic Acids Res., 43, D1057-D1063.
10. Tatusova, T. (2016) Update on genomic databases and resources at the national center for biotechnology information. Methods Mol. Biol., 1415, 3-30.
11. Aken, B.L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., Fernandez Banet, J., Billis, K., Garcia Giron, C., Hourlier, T. et al. (2016) The Ensembl gene annotation system. Database (Oxford), 2016, baw093.
12. Forbes, S.A., Beare, D., Gunasekaran, P., Leung, K., Bindal, N., Boutselakis, H., Ding, M., Bamford, S., Cole, C., Ward, S. et al. (2015) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res., 43, D805-D811.
13. Liebel, U., Starkuviene, V., Erfle, H., Simpson, J.C., Poustka, A., Wiemann, S. and Pepperkok, R. (2003) A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Lett., 554, 394-398.
14. Simpson, J.C., Wellenreuther, R., Poustka, A., Pepperkok, R. and Wiemann, S. (2000) Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep., 1, 287-292.
15. Sigal, A., Danon, T., Cohen, A., Milo, R., Geva-Zatorsky, N., Lustig, G., Liron, Y., Alon, U. and Perzov, N. (2007) Generation of a fluorescently labeled endogenous protein library in living human cells. Nat. Protoc., 2, 1515-1527.
16. Orchard, S., Ammari, M., Aranda, B., Breuza, L., Briganti, L., Broackes-Carter, F., Campbell, N.H., Chavali, G., Chen, C., del-Toro, N. et al. (2014) The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 42, D358-D363.
17. Deutsch, E.W., Sun, Z., Campbell, D., Kusebauch, U., Chu, C.S., Mendoza, L., Shteynberg, D., Omenn, G.S. and Moritz, R.L. (2015) State of the human proteome in 2014/2015 as viewed through peptideatlas: enhancing accuracy and coverage through the AtlasProphet. J. Proteome Res., 14, 3461-3473.
18. Zhang, Y., Wang, J., Ding, M. and Yu, Y. (2013) Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome. Nat. Methods, 10, 981-984.
19. Sun, G., Jiang, M., Zhou, T., Guo, Y., Cui, Y., Guo, X. and Sha, J. (2014) Insights into the lysine acetylproteome of human sperm. J. Proteomics, 109, 199-211.
20. The, Gene Ontology Consortium(2015) Gene ontology consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
21. Smith, C.L. and Eppig, J.T. (2012) The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm. Genome, 23, 653-668.
22. Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., Turner, S., Swainston, N., Mendes, P. and Steinbeck, C. (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res., 44, D1214-D1219.
23. Hinard, V., Britan, A., Rougier, J.S., Bairoch, A., Abriel, H. and Gaudet, P. (2016) ICEPO: the ion channel electrophysiology ontology. Database (Oxford), 2016, baw017.
24. Chibucos, M.C., Mungall, C.J., Balakrishnan, R., Christie, K.R., Huntley, R.P., White, O., Blake, J.A., Lewis, S.E. and Giglio, M. (2014) Standardized description of scientific evidence using the evidence ontology (ECO). Database (Oxford), 2014, bau075.
25. Deutsch, E.W., Overall, C.M., Van Eyk, J.E., Baker, M.S., Paik, Y.K., Weintraub, S.T., Lane, L., Martens, L., Vandenbrouck, Y., Kusebauch, U. et al. (2016) Human proteome project mass spectrometry data interpretation guidelines 2.1. J. Proteome Res., 15, 3961-3970.