The TissueNet database of human tissue protein-protein interactions

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Barshir, Ruth ^a   Basha, Omer ^a   Eluk, Amir ^a   Smoly, Ilan Y ^a   Lan, Alexander ^a   Yeger Lotem, Esti ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER AIDED DESIGN; COMPUTER INTERFACE; COMPUTER NETWORK; COMPUTER SIMULATION; DNA MICROARRAY; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; INFORMATION RETRIEVAL; INFORMATION SERVICE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TISSUENET DATABASE;

DATABASES, PROTEIN; GENE EXPRESSION PROFILING; HUMANS; INTERNET; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; USER-COMPUTER INTERFACE;

EID: 84876569934     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1198     Document Type: Article

References (21)

1. Schadt, E.E., Friend, S.H. and Shaywitz, D.A. (2009) A network view of disease and compound screening. Nat. Rev. Drug Discov., 8, 286-295.
2. Vidal, M., Cusick, M.E. and Barabasi, A.L. (2011) Interactome networks and human disease. Cell, 144, 986-998.
3. Berggard, T., Linse, S. and James, P. (2007) Methods for the detection and analysis of protein-protein interactions. Proteomics, 7, 2833-2842.
4. Stark, C., Breitkreutz, B.J., Chatr-Aryamontri, A., Boucher, L., Oughtred, R., Livstone, M.S., Nixon, J., Van Auken, K., Wang, X., Shi, X. et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res., 39, D698-D704.
5. Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U. and Eisenberg, D. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
6. Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A.T., Kerrien, S., Khadake, J. et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res., 38, D525-D531.
7. Ceol, A., Chatr Aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L. and Cesareni, G. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res., 38, D532-D539.
8. Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067.
9. Ramskold, D., Wang, E.T., Burge, C.B. and Sandberg, R. (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol., 5, e1000598.
10. Bossi, A. and Lehner, B. (2009) Tissue specificity and the human protein interaction network. Mol. Syst. Biol., 5, 260.
11. Emig, D., Kacprowski, T. and Albrecht, M. (2011) Measuring and analyzing tissue specificity of human genes and protein complexes. EURASIP J. Bioinform. Syst. Biol., 2011, 5.
12. Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny Stein, T., Shmoish, M., Nativ, N., Bahir, I., Doniger, T., Krug, H. et al. (2010) GeneCards Version 3: the human gene integrator. Database (Oxford), 2010, baq020.
13. 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.
14. Wu, C., Orozco, C., Boyer, J., Leglise, M., Goodale, J., Batalov, S., Hodge, C.L., Haase, J., Janes, J., Huss, J.W. III et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol., 10, R130.
15. Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E. et al. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics, 21, 650-659.
16. Berglund, L., Bjorling, E., Oksvold, P., Fagerberg, L., Asplund, A., Szigyarto, C.A., Persson, A., Ottosson, J., Wernerus, H., Nilsson, P. et al. (2008) A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol. Cell. Proteomics, 7, 2019-2027.
17. Bradley, R.K., Merkin, J., Lambert, N.J. and Burge, C.B. (2012) Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol., 10, e1001229.
18. Guberman, J.M., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R.J. et al. (2011) BioMart central portal: an open database network for the biological community. Database (Oxford), 2011, bar041.
19. Lopes, C.T., Franz, M., Kazi, F., Donaldson, S.L., Morris, Q. and Bader, G.D. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.
20. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
21. Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, L.J. and Bork, P. (2012) STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res., 40, D876-D880.