GenomewidePDB 2.0: A newly upgraded versatile proteogenomic database for the chromosome-centric human proteome project

Journal of Proteome Research

Volumn 14, Issue 9, 2015, Pages 3710-3719

  Jeong, Seul Ki ^a   Hancock, William S ^b   Paik, Young Ki ^a,c  

^a Yonsei University   (South Korea)

^b NORTHEASTERN UNIVERSITY   (United States)

^c Yonsei University   (South Korea)

Author keywords

alternative splicing; Chromosome Centric Human Proteome Project; database; GenomewidePDB; missing protein; proteomics

Indexed keywords

PEPTIDE; PROTEOME;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CHROMOSOME; DATA PROCESSING; GENETIC ASSOCIATION; HUMAN; HUMAN GENOME PROJECT; HUMAN TISSUE; INFORMATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEOMICS; STRUCTURAL PROTEOMICS; CHROMOSOMAL MAPPING; GENETIC DATABASE; HUMAN GENOME; MOLECULAR GENETICS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; CHROMOSOME MAPPING; DATABASES, GENETIC; DATABASES, PROTEIN; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE DATA; PROTEOME; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84941122690     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00541     Document Type: Article

References (33)

1. Paik, Y. K.; Jeong, S. K.; Omenn, G. S.; Uhlen, M.; Hanash, S. et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome Nat. Biotechnol. 2012, 30, 221-3 10.1038/nbt.2152
2. Paik, Y. K.; Omenn, G. S.; Uhlen, M.; Hanash, S.; Marko-Varga, G. et al. Standard guidelines for the Chromosome-centric Human Proteome Project J. Proteome Res. 2012, 11 (4) 2005-13 10.1021/pr200824a
3. Hancock, W.; Omenn, G. S.; Legrain, P.; Paik, Y. K. Proteomics, human proteome project, and chromosomes J. Proteome Res. 2011, 10, 210 10.1021/pr101099h
4. Lane, L.; Bairoch, A.; Beavis, R. C.; Deutsch, E. W.; Gaudet, P. et al. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins J. Proteome Res. 2014, 13, 15-20 10.1021/pr401144x
5. Marko-Varga, G.; Omenn, G. S.; Paik, Y. K.; Hancock, W. S. A first step toward completion of a genome-wide characterization of the human proteome J. Proteome Res. 2013, 12, 1-5 10.1021/pr301183a
6. Paik, Y. K.; Omenn, G. S.; Thongboonkerd, V.; Marko-Varga, G.; Hancock, W. S. et al. Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II J. Proteome Res. 2014, 13, 1-4 10.1021/pr4011958
7. Kim, M. S.; Pinto, S. M.; Getnet, D.; Nirujogi, R. S.; Manda, S. S. et al. A draft map of the human proteome Nature 2014, 509, 575-81 10.1038/nature13302
8. Uhlén, M.; Fagerberg, L.; Hallström, B. M.; Lindskog, C.; Oksvold, P. et al. Proteomics. Tissue-based map of the human proteome Science 2015, 347, 1260419 10.1126/science.1260419
9. Wilhelm, M.; Schlegl, J.; Hahne, H.; Gholami, A. M.; Lieberenz, M. et al. Mass-spectrometry-based draft of the human proteome Nature 2014, 509, 582-7 10.1038/nature13319
10. Gaudet, P.; Michel, P. A.; Zahn-Zabal, M.; Cusin, I.; Duek, P. D. et al. The neXtProt knowledgebase on human proteins: current status Nucleic Acids Res. 2015, 43, D764-70 10.1093/nar/gku1178
11. Deutsch, E. W.; Sun, Z.; Campbell, D.; Kusebauch, U.; Chu, C. S. et al. The State of the Human Proteome in 2014/2015 as viewed through PeptideAtlas: enhancing accuracy and coverage through the AtlasProphet J. Proteome Res. 2015, 150724142438005 10.1021/acs.jproteome.5b00500
12. Savitski, M. M.; WIlhelm, M.; Hahne, H.; Kuster, B.; Bantscheff, M. et al. A scalable approach for protein false discovery rate estimation in large proteomic data sets Mol. Cell. Proteomics 2015, mcp.M114.046995 10.1074/mcp.M114.046995
13. Lee, H. J.; Jeong, S. K.; Na, K.; Lee, M. J.; Lee, S. H. et al. Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project J. Proteome Res. 2013, 12, 2458-66 10.1021/pr301040g
14. Brunner, E.; Ahrens, C. H.; Mohanty, S.; Baetschmann, H.; Loevenich, S. et al. A high-quality catalog of the Drosophila melanogaster proteome Nat. Biotechnol. 2007, 25, 576-83 10.1038/nbt1300
15. Nilsen, T. W.; Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing Nature 2010, 463, 457-63 10.1038/nature08909
16. Omenn, G. S.; Menon, R.; Zhang, Y. Innovations in proteomic profiling of cancers: Alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology J. Proteomics 2013, 90, 28-37 10.1016/j.jprot.2013.04.007
17. Menon, R.; Zhang, Q.; Zhang, Y.; Fermin, D.; Bardeesy, N. et al. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer Cancer Res. 2009, 69, 300-9 10.1158/0008-5472.CAN-08-2145
18. Heydarian, M.; McCaffrey, T.; Florea, L.; Yang, Z.; Ross, M. M. et al. Novel splice variants of sFlt1 are upregulated in preeclampsia Placenta 2009, 30, 250-5 10.1016/j.placenta.2008.12.010
19. Sela, S.; Itin, A.; Natanson-Yaron, S.; Greenfield, C.; Goldman-Wohl, D. et al. A novel human-specific soluble vascular endothelial growth factor receptor 1: cell-type-specific splicing and implications to vascular endothelial growth factor homeostasis and preeclampsia Circ. Res. 2008, 102, 1566-74 10.1161/CIRCRESAHA.108.171504
20. Menon, R.; Im, H.; Zhang, E. Y.; Wu, S. L.; Chen, R. et al. Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes J. Proteome Res. 2014, 13, 212-27 10.1021/pr400773v
21. Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11, 1114-25 10.1038/nmeth.3144
22. Ahlf, D. R.; Thomas, P. M.; Kelleher, N. L. Developing top down proteomics to maximize proteome and sequence coverage from cells and tissues Curr. Opin. Chem. Biol. 2013, 17, 787-94 10.1016/j.cbpa.2013.07.028
23. Hüttenhain, R.; Soste, M.; Selevsek, N.; Röst, H.; Sethi, A. et al. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics Sci. Transl. Med. 2012, 4, 142ra94 10.1126/scitranslmed.3003989
24. Boersema, P. J.; Kahraman, A.; Picotti, P. Proteomics beyond large-scale protein expression analysis Curr. Opin. Biotechnol. 2015, 34C, 162-170 10.1016/j.copbio.2015.01.005
25. Garcia, B. A, Top Down mass spectrometry J. Am. Soc. Mass Spectrom. 2010, 21, 193-202 10.1016/j.jasms.2009.10.014
26. Jeong, S. K.; Lee, H. J.; Na, K.; Cho, J. Y.; Lee, M. J. et al. GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes J. Proteome Res. 2013, 12, 106-11 10.1021/pr3009447
27. Hamosh, A.; Scott, A. F.; Amberger, J. S.; Bocchini, C. A.; McKusick, V. A. et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders Nucleic Acids Res. 2005, 33, D514-7 10.1093/nar/gki033
28. Futreal, P. A.; Coin, L.; Marshall, M.; Down, T.; Hubbard, T. et al. A census of human cancer genes Nat. Rev. Cancer 2004, 4, 177-83 10.1038/nrc1299
29. Uhlen, M.; Ponten, F. Antibody-based proteomics for human tissue profiling Mol. Cell. Proteomics 2005, 4, 384-93 10.1074/mcp.R500009-MCP200
30. Wheeler, D. L.; Church, D. M.; Federhen, S.; Lash, A. E.; Madden, T. L. et al. Database resources of the National Center for Biotechnology Nucleic Acids Res. 2003, 31, 28-33 10.1093/nar/gkg033
31. NCBI Resource Coordinators Database resources of the National Center for Biotechnology Information Nucleic Acids Res. 2015, 43, D6-17 10.1093/nar/gku1130
32. Jeong, S. K.; Na, K.; Kim, K. Y.; Kim, H.; Paik, Y. K. et al. PanelComposer: a web-based panel construction tool for multivariate analysis of disease biomarker candidates J. Proteome Res. 2012, 11, 6277-81 10.1021/pr3004387
33. Youden, W. J. Index for rating diagnostic tests Cancer 1950, 3, 32-5 10.1002/1097-0142(1950)3:1<32::AID-CNCR2820030106>3.0.CO;2-3