Human protein interaction networks across tissues and diseases

Frontiers in Genetics

Volumn 6, Issue Aug, 2015, Pages

  Yeger Lotem, Esti ^a   Sharan, Roded ^b  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

Disease specific network; Gene expression; Network perturbation; Protein interaction network; Tissue specific network

Indexed keywords

ALTERNATIVE RNA SPLICING; GENE MUTATION; GENE SEQUENCE; HUMAN; MICROARRAY ANALYSIS; PHENOTYPE; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; RNA PROCESSING; SHORT SURVEY;

EID: 84940982679     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2015.00257     Document Type: Short Survey

References (48)

1. Barabási, A. L., Gulbahce, N., and Loscalzo, J. (2011). Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 12, 56-68. doi: 10.1038/nrg2918.
2. Barshir, R., Basha, O., Eluk, A., Smoly, I. Y., Lan, A., and Yeger-Lotem, E. (2013). The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res. 41, D841-D844. doi: 10.1093/nar/gks1198.
3. Barshir, R., Shwartz, O., Smoly, I. Y., and Yeger-Lotem, E. (2014). Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PLoS Comput. Biol. 10:e1003632. doi: 10.1371/journal.pcbi.1003632.
4. Basha, O., Flom, D., Barshir, R., Smoly, I., Tirman, S., and Yeger-Lotem, E. (2015). MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. Nucleic Acids Res. 43, W258-W263. doi: 10.1093/nar/gkv515.
5. Bossi, A., and Lehner, B. (2009). Tissue specificity and the human protein interaction network. Mol. Syst. Biol. 5, 260. doi: 10.1038/msb.2009.17.
6. Buljan, M., Chalancon, G., Eustermann, S., Wagner, G. P., Fuxreiter, M., Bateman, A., et al. (2012). Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol. Cell 46, 871-883. doi: 10.1016/j.molcel.2012.05.039.
7. Chatr-Aryamontri, A., Breitkreutz, B. J., Oughtred, R., Boucher, L., Heinicke, S., Chen, D., et al. (2015). The BioGRID interaction database: 2015 update. Nucleic Acids Res. 43, D470-D478. doi: 10.1093/nar/gku1204.
8. de Lichtenberg, U., Jensen, L. J., Brunak, S., and Bork, P. (2005). Dynamic complex formation during the yeast cell cycle. Science 307, 724-727. doi: 10.1126/science.1105103.
9. Dezso, Z., Nikolsky, Y., Sviridov, E., Shi, W., Serebriyskaya, T., Dosymbekov, D., et al. (2008). A comprehensive functional analysis of tissue specificity of human gene expression. BMC Biol. 6:49. doi: 10.1186/1741-7007-6-49.
10. Ellis, J. D., Barrios-Rodiles, M., Colak, R., Irimia, M., Kim, T., Calarco, J. A., et al. (2012). Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol. Cell 46, 884-892. doi: 10.1016/j.molcel.2012.05.037.
11. Emig, D., and Albrecht, M. (2011). Tissue-specific proteins and functional implications. J. Proteome Res. 10, 1893-1903. doi: 10.1021/pr101132h.
12. Ewing, R. M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., et al. (2007). Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Bio. 3, 89. doi: 10.1038/msb4100134.
13. Hillier, L. D., Lennon, G., Becker, M., Bonaldo, M. F., Chiapelli, B., Chissoe, S., et al. (1996). Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6, 807-828. doi: 10.1101/gr.6.9.807.
14. Ideker, T., and Krogan, N. J. (2012). Differential network biology. Mol. Syst. Biol. 8, 565. doi: 10.1038/msb.2011.99.
15. Jongeneel, C. V., Delorenzi, M., Iseli, C., Zhou, D., Haudenschild, C. D., Khrebtukova, I., et al. (2005). An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res. 15, 1007-1014. doi: 10.1101/gr.4041005.
16. Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., et al. (2012). The IntAct molecular interaction database in 2012. Nucleic Acids Res. 40, D841-D846. doi: 10.1093/nar/gkr1088.
17. Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., et al. (2014). A draft map of the human proteome. Nature 509, 575-581. doi: 10.1038/nature13302.
18. Kiran, M., and Nagarajaram, H. A. (2013). Global versus local hubs in human protein-protein interaction network. J. Proteome Res. 12, 5436-5446. doi: 10.1021/pr4002788.
19. Lage, K., Hansen, N. T., Karlberg, E. O., Eklund, A. C., Roque, F. S., Donahoe, P. K., et al. (2008). A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc. Natl. Acad. Sci. U.S.A. 105, 20870-20875. doi: 10.1073/pnas.0810772105.
20. Lambert, J. P., Ivosev, G., Couzens, A. L., Larsen, B., Taipale, M., Lin, Z. Y., et al. (2013). Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nat. Methods 10, 1239-1245. doi: 10.1038/nmeth.2702.
21. Li, M., Zhang, J., Liu, Q., Wang, J., and Wu, F. X. (2014). Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation. BMC Med. Genomics 7(Suppl. 2):S4. doi: 10.1186/1755-8794-7-S2-S4.
22. Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., et al. (2012). MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 40, D857-D861. doi: 10.1093/nar/gkr930.
23. Lin, W. H., Liu, W. C., and Hwang, M. J. (2009). Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. BMC Syst. Biol. 3:32. doi: 10.1186/1752-0509-3-32.
24. Liu, W., Wang, J., Wang, T., and Xie, H. (2014). Construction and analyses of human large-scale tissue specific networks. PLoS ONE 9:e115074. doi: 10.1371/journal.pone.0115074.
25. Lopes, T. J., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J. F., Neumann, G., et al. (2011). Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics 27, 2414-2421. doi: 10.1093/bioinformatics/btr414.
26. Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M., Teichmann, S. A., and Gerstein, M. (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431, 308-312. doi: 10.1038/nature02782.
27. Magger, O., Waldman, Y. Y., Ruppin, E., and Sharan, R. (2012). Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput. Biol. 8:e1002690. doi: 10.1371/journal.pcbi.1002690.
28. Melé, M., Ferreira, P. G., Reverter, F., DeLuca, D. S., Monlong, J., Sammeth, M., et al. (2015). Human genomics. The human transcriptome across tissues and individuals. Science 348, 660-665. doi: 10.1126/science.aaa0355.
29. Pontén, F., Gry, M., Fagerberg, L., Lundberg, E., Asplund, A., Berglund, L., et al. (2009). A global view of protein expression in human cells, tissues, and organs. Mol. Syst. Biol. 5, 337. doi: 10.1038/msb.2009.93.
30. Ramsköld, 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. doi: 10.1371/journal.pcbi.1000598.
31. Rolland, T., Tasan, M., Charloteaux, B., Pevzner, S. J., Zhong, Q., Sahni, N., et al. (2014). A proteome-scale map of the human interactome network. Cell 159, 1212-1226. doi: 10.1016/j.cell.2014.10.050.
32. Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., et al. (2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178. doi: 10.1038/nature04209.
33. Sahni, N., Yi, S., Taipale, M., Fuxman Bass, J. I., Coulombe-Huntington, J., Yang, F., et al. (2015). Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161, 647-660. doi: 10.1016/j.cell.2015.04.013.
34. Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., et al. (2011). Global quantification of mammalian gene expression control. Nature 473, 337-342. doi: 10.1038/nature10098.
35. Sinha, A., and Nagarajaram, H. A. (2014). Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants. Proteomics 14, 2242-2248. doi: 10.1002/pmic.201400249.
36. Song, J., Wang, Z., and Ewing, R. M. (2014). Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks. Mol. Biosyst. 10, 45-53. doi: 10.1039/C3MB70417C.
37. Souiai, O., Becker, E., Prieto, C., Benkahla, A., De las Rivas, J., and Brun, C. (2011). Functional integrative levels in the human interactome recapitulate organ organization. PLoS ONE 6:e22051. doi: 10.1371/journal.pone.0022051.
38. Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F. H., Goehler, H., et al. (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957-968. doi: 10.1016/j.cell.2005.08.029.
39. Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A. 101, 6062-6067. doi: 10.1073/pnas.0400782101.
40. Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., et al. (2015). Proteomics. Tissue-based map of the human proteome. Science 347, 1260419. doi: 10.1126/science.1260419.
41. Vidal, M., Cusick, M. E., and Barabási, A. L. (2011). Interactome networks and human disease. Cell 144, 986-998. doi: 10.1016/j.cell.2011.02.016.
42. Waldman, Y. Y., Tuller, T., Shlomi, T., Sharan, R., and Ruppin, E. (2010). Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acids Res. 38, 2964-2974. doi: 10.1093/nar/gkq009.
43. Wang, X., Wei, X., Thijssen, B., Das, J., Lipkin, S. M., and Yu, H. (2012). Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat. Biotechnol. 30, 159-164. doi: 10.1038/nbt.2106.
44. Wei, X., Das, J., Fragoza, R., Liang, J., Bastos de Oliveira, F. M., Lee, H. R., et al. (2014). A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PLoS Genet. 10:e1004819. doi: 10.1371/journal.pgen.1004819.
45. Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R., Ozenberger, B. A., Ellrott, K., et al. (2013). The cancer genome atlas pan-cancer analysis project. Nat. Genet. 45, 1113-1120. doi: 10.1038/ng.2764.
46. Wilhelm, M., Schlegl, J., Hahne, H., Moghaddas Gholami, A., Lieberenz, M., Savitski, M. M., et al. (2014). Mass-spectrometry-based draft of the human proteome. Nature 509, 582-587. doi: 10.1038/nature13319.
47. Xenarios, I., Salwínski, L., Duan, X. J., Higney, P., Kim, S. M., and Eisenberg, D. (2002). DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30, 303-305. doi: 10.1093/nar/30.1.303.
48. Zhong, Q., Simonis, N., Li, Q. R., Charloteaux, B., Heuze, F., Klitgord, N., et al. (2009). Edgetic perturbation models of human inherited disorders. Mol. Syst. Biol. 5, 321. doi: 10.1038/msb.2009.80.