Tissue-specific proteins and functional implications

Journal of Proteome Research

Volumn 10, Issue 4, 2011, Pages 1893-1903

  Emig, Dorothea ^a   Albrecht, Mario ^a  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

Author keywords

alternative splicing; protein complex; protein domain; protein interaction; RNA sequencing; tissue specificity

Indexed keywords

MESSENGER RNA; SNARE PROTEIN; TRANSCRIPTION FACTOR HESX1;

ARTICLE; GENE EXPRESSION; MEMBRANE TRANSPORT; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PROCESSING; RECEPTOR BINDING; RNA SEQUENCE; SIGNAL TRANSDUCTION; TISSUE SPECIFICITY; TRANSCRIPTION REGULATION;

CELL LINE; GENE EXPRESSION REGULATION; HUMANS; ORGAN SPECIFICITY; PHARMACEUTICAL PREPARATIONS; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOMICS;

EID: 79953706019     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr101132h     Document Type: Article

References (33)

1. Lehner, B.; Fraser, A. G. Protein domains enriched in mammalian tissue-specific or widely expressed genes Trends Genet. 2004, 20, 468-472 (Pubitemid 39201064)
2. Bossi, A.; Lehner, B. Tissue specificity and the human protein interaction network Mol. Syst. Biol. 2009, 5, 260
3. Lage, K.; Hansen, N. T.; Karlberg, E. O.; Eklund, A. C.; Roque, F. S.; Donahoe, P. K.; Szallasi, Z.; Jensen, T. S.; Brunak, S. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 20870-20875
4. Tu, Z.; Wang, L.; Xu, M.; Zhou, X.; Chen, T.; Sun, F. Further understanding human disease genes by comparing with housekeeping genes and other genes BMC Genomics 2006, 7, 31
5. Eisenberg, E.; Levanon, E. Y. Human housekeeping genes are compact Trends Genet. 2003, 19, 362-365 (Pubitemid 36794535)
6. She, X.; Rohl, C. A.; Castle, J. C.; Kulkarni, A. V.; Johnson, J. M.; Chen, R. Definition, conservation and epigenetics of housekeeping and tissue-enriched genes BMC Genomics 2009, 10, 269
7. Farre, D.; Bellora, N.; Mularoni, L.; Messeguer, X.; Alba, M. M. Housekeeping genes tend to show reduced upstream sequence conservation Genome Biol. 2007, 8, R140
8. Su, A. I.; Wiltshire, T.; Batalov, S.; Lapp, H.; Ching, K. A.; Block, D.; Zhang, J.; Soden, R.; Hayakawa, M.; Kreiman, G.; Cooke, M. P.; Walker, J. R.; Hogenesch, J. B. A gene atlas of the mouse and human protein-encoding transcriptomes Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 6062-6067 (Pubitemid 38520528)
9. Zhu, J.; He, F.; Song, S.; Wang, J.; Yu, J. How many human genes can be defined as housekeeping with current expression data? BMC Genomics 2008, 9, 172
10. Emig, D.; Kacprowski, T.; Albrecht, M. Measuring and analyzing tissue specificity of human genes and protein complexes. In Proceedings of the 7th International Workshop on Computational Systems Biology (WCSB), Luxembourg, June 16-18, 2010; Vol. 51, pp 27 - 30.
11. Ramskold, 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
12. Vasmatzis, G.; Klee, E. W.; Kube, D. M.; Therneau, T. M.; Kosari, F. Quantitating tissue specificity of human genes to facilitate biomarker discovery Bioinformatics 2007, 23, 1348-1355 (Pubitemid 47050516)
13. Hubbard, T. J.; Aken, B. L.; Ayling, S.; Ballester, B.; Beal, K.; Bragin, E.; Brent, S.; Chen, Y.; Clapham, P.; Clarke, L.; Coates, G.; Fairley, S.; Fitzgerald, S.; Fernandez-Banet, J.; Gordon, L.; Graf, S.; Haider, S.; Hammond, M.; Holland, R.; Howe, K.; Jenkinson, A.; Johnson, N.; Kahari, A.; Keefe, D.; Keenan, S.; Kinsella, R.; Kokocinski, F.; Kulesha, E.; Lawson, D.; Longden, I.; Megy, K.; Meidl, P.; Overduin, B.; Parker, A.; Pritchard, B.; Rios, D.; Schuster, M.; Slater, G.; Smedley, D.; Spooner, W.; Spudich, G.; Trevanion, S.; Vilella, A.; Vogel, J.; White, S.; Wilder, S.; Zadissa, A.; Birney, E.; Cunningham, F.; Curwen, V.; Durbin, R.; Fernandez-Suarez, X. M.; Herrero, J.; Kasprzyk, A.; Proctor, G.; Smith, J.; Searle, S.; Flicek, P. Ensembl 2009 Nucleic Acids Res. 2009, 37, D690-697
14. Finn, R. D.; Tate, J.; Mistry, J.; Coggill, P. C.; Sammut, S. J.; Hotz, H. R.; Ceric, G.; Forslund, K.; Eddy, S. R.; Sonnhammer, E. L.; Bateman, A. The Pfam protein families database Nucleic Acids Res. 2008, 36, D281-288
15. Wang, E. T.; Sandberg, R.; Luo, S.; Khrebtukova, I.; Zhang, L.; Mayr, C.; Kingsmore, S. F.; Schroth, G. P.; Burge, C. B. Alternative isoform regulation in human tissue transcriptomes Nature 2008, 456, 470-476 (Pubitemid 352759009)
16. Mortazavi, A.; Williams, B. A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat. Methods 2008, 5, 621-628 (Pubitemid 351911867)
17. Yildirim, M. A.; Goh, K. I.; Cusick, M. E.; Barabasi, A. L.; Vidal, M. Drug-target network Nat. Biotechnol. 2007, 25, 1119-1126 (Pubitemid 47538114)
18. Winter, E. E.; Goodstadt, L.; Ponting, C. P. Elevated rates of protein secretion, evolution, and disease among tissue-specific genes Genome Res. 2004, 14, 54-61 (Pubitemid 38088525)
19. Maier, T.; Guell, M.; Serrano, L. Correlation of mRNA and protein in complex biological samples FEBS Lett. 2009, 583, 3966-3973
20. Vogel, C.; Abreu Rde, S.; Ko, D.; Le, S. Y.; Shapiro, B. A.; Burns, S. C.; Sandhu, D.; Boutz, D. R.; Marcotte, E. M.; Penalva, L. O. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line Mol. Syst. Biol. 2010, 6, 400
21. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242 (Pubitemid 30047768)
22. Ruepp, A.; Brauner, B.; Dunger-Kaltenbach, I.; Frishman, G.; Montrone, C.; Stransky, M.; Waegele, B.; Schmidt, T.; Doudieu, O. N.; Stumpflen, V.; Mewes, H. W. CORUM: the comprehensive resource of mammalian protein complexes Nucleic Acids Res. 2008, 36, D646-650
23. Smedley, D.; Haider, S.; Ballester, B.; Holland, R.; London, D.; Thorisson, G.; Kasprzyk, A. BioMart-biological queries made easy BMC Genomics 2009, 10, 22
24. Eden, E.; Navon, R.; Steinfeld, I.; Lipson, D.; Yakhini, Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists BMC Bioinf. 2009, 10, 48
25. Alexa, A.; Rahnenfuhrer, J.; Lengauer, T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure Bioinformatics 2006, 22, 1600-1607 (Pubitemid 43985293)
26. Chambers, A. F. MDA-MB-435 and M14 cell lines: identical but not M14 melanoma? Cancer Res. 2009, 69, 5292-5293
27. Liu, B.; Liao, J.; Rao, X.; Kushner, S. A.; Chung, C. D.; Chang, D. D.; Shuai, K. Inhibition of Stat1-mediated gene activation by PIAS1 Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 10626-10631 (Pubitemid 28413118)
28. Wysocka, J.; Myers, M. P.; Laherty, C. D.; Eisenman, R. N.; Herr, W. Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1 Genes Dev. 2003, 17, 896-911 (Pubitemid 36397377)
29. de Lichtenberg, U.; Jensen, L. J.; Brunak, S.; Bork, P. Dynamic complex formation during the yeast cell cycle Science 2005, 307, 724-727 (Pubitemid 40194642)
30. Gavin, A. C.; Aloy, P.; Grandi, P.; Krause, R.; Boesche, M.; Marzioch, M.; Rau, C.; Jensen, L. J.; Bastuck, S.; Dumpelfeld, B.; Edelmann, A.; Heurtier, M. A.; Hoffman, V.; Hoefert, C.; Klein, K.; Hudak, M.; Michon, A. M.; Schelder, M.; Schirle, M.; Remor, M.; Rudi, T.; Hooper, S.; Bauer, A.; Bouwmeester, T.; Casari, G.; Drewes, G.; Neubauer, G.; Rick, J. M.; Kuster, B.; Bork, P.; Russell, R. B.; Superti-Furga, G. Proteome survey reveals modularity of the yeast cell machinery Nature 2006, 440, 631-636
31. Reim, K.; Wegmeyer, H.; Brandstatter, J. H.; Xue, M.; Rosenmund, C.; Dresbach, T.; Hofmann, K.; Brose, N. Structurally and functionally unique complexins at retinal ribbon synapses J. Cell Biol. 2005, 169, 669-680 (Pubitemid 41002859)
32. Dasen, J. S.; Barbera, J. P.; Herman, T. S.; Connell, S. O.; Olson, L.; Ju, B.; Tollkuhn, J.; Baek, S. H.; Rose, D. W.; Rosenfeld, M. G. Temporal regulation of a paired-like homeodomain repressor/TLE corepressor complex and a related activator is required for pituitary organogenesis Genes Dev. 2001, 15, 3193-3207 (Pubitemid 33115682)
33. Venkatesan, K.; Rual, J. F.; Vazquez, A.; Stelzl, U.; Lemmens, I.; Hirozane-Kishikawa, T.; Hao, T.; Zenkner, M.; Xin, X.; Goh, K. I.; Yildirim, M. A.; Simonis, N.; Heinzmann, K.; Gebreab, F.; Sahalie, J. M.; Cevik, S.; Simon, C.; de Smet, A. S.; Dann, E.; Smolyar, A.; Vinayagam, A.; Yu, H.; Szeto, D.; Borick, H.; Dricot, A.; Klitgord, N.; Murray, R. R.; Lin, C.; Lalowski, M.; Timm, J.; Rau, K.; Boone, C.; Braun, P.; Cusick, M. E.; Roth, F. P.; Hill, D. E.; Tavernier, J.; Wanker, E. E.; Barabasi, A. L.; Vidal, M. An empirical framework for binary interactome mapping Nat. Methods 2009, 6, 83-90