A chromosome-centric analysis of antibodies directed toward the human proteome using antibodypedia

Journal of Proteome Research

Volumn 13, Issue 3, 2014, Pages 1669-1676

  Alm, Tove ^a   Von Feilitzen, Kalle ^a   Lundberg, Emma ^a   Sivertsson, Åsa ^a   Uhlén, Mathias ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

Affinity reagents; Antibodies; Antibodypedia; Human proteome

Indexed keywords

ANTIBODY; PROTEOME;

ARTICLE; CHROMOSOME; CHROMOSOME ANALYSIS; DATA BASE; GENOME; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN TARGETING;

ANTIBODIES; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN; DATABASES, PROTEIN; GENOME, HUMAN; HUMAN GENOME PROJECT; HUMANS; PROTEOME; PROTEOMICS; SOFTWARE;

EID: 84896795822     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr4011525     Document Type: Article

References (25)

1. Bordeaux, J.; Welsh, A. W.; Agarwal, S.; Killiam, E.; Baquero, M. T.; Hanna, J. A.; Anagnostou, V. K.; Rimm, D. L. Antibody validation BioTechniques 2010, 48, 197-209
2. Berglund, L. A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies Mol. Cell. Proteomics 2008, 7, 2019-2027
3. Hanash, S. The Human Proteome Organization: A Mission to Advance Proteome Knowledge Mol. Cell. Proteomics 2002, 1, 413-414
4. Uhlen, M.; Oksvold, P.; Fagerberg, L.; Lundberg, E.; Jonasson, K.; Forsberg, M.; Zwahlen, M.; Kampf, C.; Wester, K.; Hober, S.; Wernerus, H.; Björling, L.; Ponten, F. Towards a knowledge-based Human Protein Atlas Nat. Biotechnol. 2010, 28, 1248-1250
5. Legrain, P. The human proteome project: Current state and future direction Mol. Cell. Proteomics 2011, M111.009993
6. A gene-centric human proteome project: HUPO-the Human Proteome organization. Mol. Cell. Proteomics 2010, 9, 427-429.
7. Desiere, F.; Deutsch, E. W.; King, N. L.; Nesvizhskii, A. I.; Mallick, P.; Eng, J.; Chen, S.; Eddes, J.; Loevenich, S. N.; Aebersold, R. The PeptideAtlas project Nucleic Acids Res. 2006, 34, D655-658
8. Farrah, T.; Deutsch, E. W.; Hoopmann, M. R.; Hallows, J. L.; Sun, Z.; Huang, C.-Y.; Moritz, R. L. The state of the human proteome in 2012 as viewed through PeptideAtlas J. Proteome Res. 2013, 12, 162-171
9. Uhlén, M. A human protein atlas for normal and cancer tissues based on antibody proteomics Mol. Cell. Proteomics 2005, 4, 1920-1932
10. Lane, L.; Argoud-Puy, G.; Britan, A.; Cusin, I.; Duek, P. D.; Evalet, O.; Gateau, A.; Gaudet, P.; Gleizes, A.; Masselot, A.; Zwahlen, C.; Bairoch, A. neXtProt: a knowledge platform for human proteins Nucleic Acids Res. 2012, 40, D76-83
11. Gaudet, P.; Argoud-Puy, G.; Cusin, I.; Duek, P.; Evalet, O.; Gateau, A.; Gleizes, A.; Pereira, M.; Zahn-Zabal, M.; Zwahlen, C.; Bairoch, A.; Lane, L. neXtProt: organizing protein knowledge in the context of human proteome projects J. Proteome Res. 2013, 12, 293-298
12. Paik, Y.-K. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome Nat. Biotechnol. 2012, 30, 221-223
13. Aebersold, R.; Bader, G. D.; Edwards, A. M.; van Eyk, J. E.; Kussmann, M.; Qin, J.; Omenn, G. S. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community J. Proteome Res. 2013, 12, 23-27
14. Paik, Y.-K. Standard guidelines for the chromosome-centric human proteome project J. Proteome Res. 2012, 11, 2005-2013
15. 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
16. Birney, E. An overview of Ensembl Genome Res. 2004, 14, 925-928
17. Flicek, P. Ensembl 2013 Nucleic Acids Res. 2013, 41, D48-55
18. Bjorling, E.; Uhlen, M. Antibodypedia, a portal for sharing antibody and antigen validation data Mol. Cell. Proteomics 2008, 7, 2028-2037
19. The UniProt Consortium. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013, 41, D43-47.
20. Tebbutt, N.; Pedersen, M. W.; Johns, T. G. Targeting the ERBB family in cancer: couples therapy Nat. Rev. Cancer 2013, 13, 663-673
21. Uhlen, M.; Ponten, F. Antibody-based proteomics for human tissue profiling Mol. Cell. Proteomics 2005, 4, 384-393
22. Edwards, A. M.; Isserlin, R.; Bader, G. D.; Frye, S. V.; Willson, T. M.; Yu, F. H. Too many roads not taken Nature 2011, 470, 163-165
23. Ramsköld, D.; Wang, E. T.; Burge, C. B.; Sandberg, R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data PLoS Comput. Biol. 2009, 5, e1000598
24. Pontén, F. A global view of protein expression in human cells, tissues, and organs Mol. Syst. Biol. 2009, 5, 337
25. Lundberg, E.; Fagerberg, L.; Klevebring, D.; Matic, I.; Geiger, T.; Cox, J.; Algenäs, C.; Lundeberg, J.; Mann, M.; Uhlen, M. Defining the transcriptome and proteome in three functionally different human cell lines Mol. Syst. Biol. 2010, 6, 450