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2014 | OriginalPaper | Buchkapitel

19. Path Finding in Biological Networks

verfasst von : Lore Cloots, Dries De Maeyer, Kathleen Marchal

Erschienen in: Springer Handbook of Bio-/Neuroinformatics

Verlag: Springer Berlin Heidelberg

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Abstract

Understanding the cellular behavior from a systems perspective requires the identification of functional and physical interactions among diverse molecular entities in a cell (i.e., DNA/RNA, proteins, and metabolites). The most straightforward way to represent such datasets is by means of molecular networks of which nodes correspond to molecular entities and edges to the interactions amongst those entities. Nowadays with large amounts of interaction data being generated, genome-wide networks can be created for an increasing number of organisms. These networks can be exploited to study a molecular entity like a protein in a wider context than just in isolation and provide a way of representing our knowledge of the system as a whole. On the other hand, viewing a single entity or an experimental dataset in the light of an interaction network can reveal previous unknown insights in biological processes.

In this chapter we focus on different approaches that have been developed to reveal the functional state of a network, or to find an explanation for the observations in functional data through paths in the network. In addition we give an overview of the different omics datasets and data-integration techniques that can be used to build integrated biological networks.

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Vorheriges Kapitel Kernel Methods and Applications in Bioinformatics

Nächstes Kapitel Inferring Transcription Networks from Data

19.1.

U. Alon: Biological networks: The tinkerer as an engineer, Science 301(5641), 1866–1867 (2003)CrossRef

19.2.

R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon: Network motifs: Simple building blocks of complex networks, Science 298(5594), 824–827 (2002)CrossRef

19.3.

U. Alon: Network motifs: Theory and experimental approaches, Nat. Rev. Genet. 8(6), 450–461 (2007)CrossRef

19.4.

Y. Ho, A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, P. Taylor, K. Bennett, K. Boutilier, L. Yang, C. Wolting, I. Donaldson, S. Schandorff, J. Shewnarane, M. Vo, J. Taggart, M. Goudreault, B. Muskat, C. Alfarano, D. Dewar, Z. Lin, K. Michalickova, A.R. Willems, H. Sassi, P.A. Nielsen, K.J. Rasmussen, J.R. Andersen, L.E. Johansen, L.H. Hansen, H. Jespersen, A. Podtelejnikov, E. Nielsen, J. Crawford, V. Poulsen, B.D. Sørensen, J. Matthiesen, R.C. Hendrickson, F. Gleeson, T. Pawson, M.F. Moran, D. Durocher, M. Mann, C.W. Hogue, D. Figeys, M. Tyers: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Nature 415(6868), 180–183 (2002)CrossRef

19.5.

T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, Y. Sakaki: A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proc. Natl. Acad. Sci. USA 98(8), 4569–4574 (2001)CrossRef

19.6.

N.J. Krogan, G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, S. Pu, N. Datta, A.P. Tikuisis, T. Punna, J.M. Peregrín-Alvarez, M. Shales, X. Zhang, M. Davey, M.D. Robinson, A. Paccanaro, J.E. Bray, A. Sheung, B. Beattie, D.P. Richards, V. Canadien, A. Lalev, F. Mena, P. Wong, A. Starostine, M.M. Canete, J. Vlasblom, S. Wu, C. Orsi, S.R. Collins, S. Chandran, R. Haw, J.J. Rilstone, K. Gandi, N.J. Thompson, G. Musso, P. St. Onge, S. Ghanny, M.H. Lam, G. Butland, A.M. Altaf-Ul, S. Kanaya, A. Shilatifard, E. OʼShea, J.S. Weissman, C.J. Ingles, T.R. Hughes, J. Parkinson, M. Gerstein, S.J. Wodak, A. Emili, J.F. Greenblatt: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae, Nature 440(7084), 637–643 (2006)CrossRef

19.7.

P. Uetz, L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, J.M. Rothberg: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature 403(6770), 623–627 (2000)CrossRef

19.8.

A.C. Gavin, M. Bösche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, A.M. Michon, C.M. Cruciat, M. Remor, C. Höfert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M.A. Heurtier, R.R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, G. Superti-Furga: Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature 415(6868), 141–147 (2002)CrossRef

19.9.

S. Li, C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.O. Vidalain, J.D. Han, A. Chesneau, T. Hao, D.S. Goldberg, N. Li, M. Martinez, J.F. Rual, P. Lamesch, L. Xu, M. Tewari, S.L. Wong, L.V. Zhang, G.F. Berriz, L. Jacotot, P. Vaglio, J. Reboul, T. Hirozane-Kishikawa, Q. Li, H.W. Gabel, A. Elewa, B. Baumgartner, D.J. Rose, H. Yu, S. Bosak, R. Sequerra, A. Fraser, S.E. Mango, W.M. Saxton, S. Strome, S. van den Heuvel, F. Piano, J. Vandenhaute, C. Sardet, M. Gerstein, L. Doucette-Stamm, K.C. Gunsalus, J.W. Harper, M.E. Cusick, F.P. Roth, D.E. Hill, M. Vidal: A map of the interactome network of the metazoan C. elegans, Science 303(5657), 540–543 (2004)CrossRef

19.10.

E. Formstecher, S. Aresta, V. Collura, A. Hamburger, A. Meil, A. Trehin, C. Reverdy, V. Betin, S. Maire, C. Brun, B. Jacq, M. Arpin, Y. Bellaiche, S. Bellusci, P. Benaroch, M. Bornens, R. Chanet, P. Chavrier, O. Delattre, V. Doye, R. Fehon, G. Faye, T. Galli, J.A. Girault, B. Goud, J. de Gunzburg, L. Johannes, M.P. Junier, V. Mirouse, A. Mukherjee, D. Papadopoulo, F. Perez, A. Plessis, C. Rossé, S. Saule, D. Stoppa-Lyonnet, A. Vincent, M. White, P. Legrain, J. Wojcik, J. Camonis, L. Daviet: Protein interaction mapping: A Drosophila case study, Genome Res. 15(3), 376–384 (2005)CrossRef

19.11.

L. Giot, J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y.L. Hao, C.E. Ooi, B. Godwin, E. Vitols, G. Vijayadamodar, P. Pochart, H. Machineni, M. Welsh, Y. Kong, B. Zerhusen, R. Malcolm, Z. Varrone, A. Collis, M. Minto, S. Burgess, L. McDaniel, E. Stimpson, F. Spriggs, J. Williams, K. Neurath, N. Ioime, M. Agee, E. Voss, K. Furtak, R. Renzulli, N. Aanensen, S. Carrolla, E. Bickelhaupt, Y. Lazovatsky, A. DaSilva, J. Zhong, C.A. Stanyon, R.L. Finley Jr., K.P. White, M. Braverman, T. Jarvie, S. Gold, M. Leach, J. Knight, R.A. Shimkets, M.P. McKenna, J. Chant, J.M. Rothberg: A protein interaction map of Drosophila melanogaster, Science 302(5651), 1727–1736 (2003)CrossRef

19.12.

J.F. Rual, K. Venkatesan, T. Hao, T. Hirozane-Kishikawa, A. Dricot, N. Li, G.F. Berriz, F.D. Gibbons, M. Dreze, N. Ayivi-Guedehoussou, N. Klitgord, C. Simon, M. Boxem, S. Milstein, J. Rosenberg, D.S. Goldberg, L.V. Zhang, S.L. Wong, G. Franklin, S. Li, J.S. Albala, J. Lim, C. Fraughton, E. Llamosas, S. Cevik, C. Bex, P. Lamesch, R.S. Sikorski, J. Vandenhaute, H.Y. Zoghbi, A. Smolyar, S. Bosak, R. Sequerra, L. Doucette-Stamm, M.E. Cusick, D.E. Hill, F.P. Roth, M. Vidal: Towards a proteome-scale map of the human protein-protein interaction network, Nature 437(7062), 1173–1178 (2005)CrossRef

19.13.

U. Stelzl, U. Worm, M. Lalowski, C. Haenig, F.H. Brembeck, H. Goehler, M. Stroedicke, M. Zenkner, A. Schoenherr, S. Koeppen, J. Timm, S. Mintzlaff, C. Abraham, N. Bock, S. Kietzmann, A. Goedde, E. Toksöz, A. Droege, S. Krobitsch, B. Korn, W. Birchmeier, H. Lehrach, E.E. Wanker: A human protein-protein interaction network: A resource for annotating the proteome, Cell 122(6), 957–968 (2005)CrossRef

19.14.

T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G. Jennings, H.L. Murray, D.B. Gordon, B. Ren, J.J. Wyrick, J.B. Tagne, T.L. Volkert, E. Fraenkel, D.K. Gifford, R.A. Young: Transcriptional regulatory networks in Saccharomyces cerevisiae, Science 298(5594), 799–804 (2002)CrossRef

19.15.

C.T. Harbison, D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. Macisaac, T.W. Danford, N.M. Hannett, J.B. Tagne, D.B. Reynolds, J. Yoo, E.G. Jennings, J. Zeitlinger, D.K. Pokholok, M. Kellis, P.A. Rolfe, K.T. Takusagawa, E.S. Lander, D.K. Gifford, E. Fraenkel, R.A. Young: Transcriptional regulatory code of a eukaryotic genome, Nature 431(7004), 99–104 (2004)CrossRef

19.16.

S.E. Celniker, L.A. Dillon, M.B. Gerstein, K.C. Gunsalus, S. Henikoff, G.H. Karpen, M. Kellis, E.C. Lai, J.D. Lieb, D.M. MacAlpine, G. Micklem, F. Piano, M. Snyder, L. Stein, K.P. White, R.H. Waterston, modENCODE Consortium: Unlocking the secrets of the genome, Nature 459(7249), 927–930 (2009)CrossRef

19.17.

R. Aebersold, M. Mann: Mass spectrometry-based proteomics, Nature 422(6928), 198–207 (2003)CrossRef

19.18.

M. Kanehisa, S. Goto, M. Furumichi, M. Tanabe, M. Hirakawa: KEGG for representation and analysis of molecular networks involving diseases and drugs, Nucleic Acids Res. 38(Database issue), D355–360 (2010)CrossRef

19.19.

R. Caspi, T. Altman, J.M. Dale, K. Dreher, C.A. Fulcher, F. Gilham, P. Kaipa, A.S. Karthikeyan, A. Kothari, M. Krummenacker, M. Latendresse, L.A. Mueller, S. Paley, L. Popescu, A. Pujar, A.G. Shearer, P. Zhang, P.D. Karp: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Res. 38(Database issue), D473–479 (2010)CrossRef

19.20.

J. Schellenberger, J.O. Park, T.M. Conrad, B.O. Palsson: BiGG: A biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions, BMC Bioinformatics 11, 213 (2010)CrossRef

19.21.

C. Stark, B.J. Breitkreutz, A. Chatr-Aryamontri, L. Boucher, R. Oughtred, M.S. Livstone, J. Nixon, K. Van Auken, X. Wang, X. Shi, T. Reguly, J.M. Rust, A. Winter, K. Dolinski, M. Tyers: The BioGRID interaction database: 2011 update, Nucleic Acids Res. 39(Database issue), D698–704 (2011)CrossRef

19.22.

G.D. Bader, D. Betel, C.W. Hogue: BIND: The biomolecular interaction network database, Nucleic Acids Res. 31(1), 248–250 (2003)CrossRef

19.23.

I. Xenarios, L. Salwinski, X.J. Duan, P. Higney, S.M. Kim, D. Eisenberg: DIP, the Database of interacting proteins: A research tool for studying cellular networks of protein interactions, Nucleic Acids Res. 30(1), 303–305 (2002)CrossRef

19.24.

A. Ceol, A. Chatr Aryamontri, L. Licata, D. Peluso, L. Briganti, L. Perfetto, L. Castagnoli, G. Cesareni: MINT, the molecular interaction database: 2009 update, Nucleic Acids Res. 38(Database issue), D532–539 (2010)CrossRef

19.25.

H.W. Mewes, A. Ruepp, F. Theis, T. Rattei, M. Walter, D. Frishman, K. Suhre, M. Spannagl, K.F. Mayer, V. Stumpflen, A. Antonov: MIPS: Curated databases and comprehensive secondary data resources in 2010, Nucleic Acids Res. 39(Database issue), D220–224 (2011)CrossRef

19.26.

C. von Mering, M. Huynen, D. Jaeggi, S. Schmidt, P. Bork, B. Snel: STRING: A database of predicted functional associations between proteins, Nucleic Acids Res. 31(1), 258–261 (2003)CrossRef

19.27.

R. Goel, B. Muthusamy, A. Pandey, T.S. Prasad: Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology, Mol. Biotechnol. 48(1), 87–95 (2011)CrossRef

19.28.

A. Ruepp, B. Waegele, M. Lechner, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, H.W. Mewes: CORUM: The comprehensive resource of mammalian protein complexes – 2009, Nucleic Acids Res. 38(Database issue), D497–501 (2010)CrossRef

19.29.

E. Wingender: The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation, Brief Bioinf. 9(4), 326–332 (2008)CrossRef

19.30.

P.E. Hodges, A.H. McKee, B.P. Davis, W.E. Payne, J.I. Garrels: The yeast proteome database (YPD): A model for the organization and presentation of genome-wide functional data, Nucleic Acids Res. 27(1), 69–73 (1999)CrossRef

19.31.

C.Y. Yang, C.H. Chang, Y.L. Yu, T.C. Lin, S.A. Lee, C.C. Yen, J.M. Yang, J.M. Lai, Y.R. Hong, T.L. Tseng, K.M. Chao, C.Y. Huang: PhosphoPOINT: A comprehensive human kinase interactome and phospho-protein database, Bioinformatics 24(16), i14–20 (2008)CrossRef

19.32.

P.V. Hornbeck, I. Chabra, J.M. Kornhauser, E. Skrzypek, B. Zhang: PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation, Proteomics 4(6), 1551–1561 (2004)CrossRef

19.33.

G.R. Cochrane, M.Y. Galperin: The 2010 nucleic acids research database issue and online database collection: A community of data resources, Nucleic Acids Res. 38(Database issue), D1–4 (2010)CrossRef

19.34.

G.D. Bader, M.P. Cary, C. Sander: Pathguide: A pathway resource list, Nucleic Acids Res. 34(Database issue), D504–506 (2006)CrossRef

19.35.

A. Beyer, C. Workman, J. Hollunder, D. Radke, U. Moller, T. Wilhelm, T. Ideker: Integrated assessment and prediction of transcription factor binding, PLoS Comput. Biol. 2(6), e70 (2006)CrossRef

19.36.

G.T. Hart, A.K. Ramani, E.M. Marcotte: How complete are current yeast and human protein-protein interaction networks?, Genome Biol. 7(11), 120 (2006)CrossRef

19.37.

F. Ramirez, A. Schlicker, Y. Assenov, T. Lengauer, M. Albrecht: Computational analysis of human protein interaction networks, Proteomics 7(15), 2541–2552 (2007)CrossRef

19.38.

C. von Mering, R. Krause, B. Snel, M. Cornell, S.G. Oliver, S. Fields, P. Bork: Comparative assessment of large-scale data sets of protein-protein interactions, Nature 417(6887), 399–403 (2002)CrossRef

19.39.

C.M. Bishop: Pattern Recognition and Machine Learning (Springer, New York 2006)MATH

19.40.

D. Ucar, A. Beyer, S. Parthasarathy, C.T. Workman: Predicting functionality of protein-DNA interactions by integrating diverse evidence, Bioinformatics 25(12), i137–i144 (2009)CrossRef

19.41.

J.S. Bader, A. Chaudhuri, J.M. Rothberg, J. Chant: Gaining confidence in high-throughput protein interaction networks, Nat. Biotechnol. 22(1), 78–85 (2004)CrossRef

19.42.

R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N.J. Krogan, S. Chung, A. Emili, M. Snyder, J.F. Greenblatt, M. Gerstein: A Bayesian networks approach for predicting protein-protein interactions from genomic data, Science 302(5644), 449–453 (2003)CrossRef

19.43.

D.R. Rhodes, S.A. Tomlins, S. Varambally, V. Mahavisno, T. Barrette, S. Kalyana-Sundaram, D. Ghosh, A. Pandey, A.M. Chinnaiyan: Probabilistic model of the human protein-protein interaction network, Nat. Biotechnol. 23(8), 951–959 (2005)CrossRef

19.44.

M.S. Scott, G.J. Barton: Probabilistic prediction and ranking of human protein-protein interactions, BMC Bioinformatics 8, 239 (2007)CrossRef

19.45.

R. Sharan, S. Suthram, R.M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sittler, R.M. Karp, T. Ideker: Conserved patterns of protein interaction in multiple species, Proc. Natl. Acad. Sci. USA 102(6), 1974–1979 (2005)CrossRef

19.46.

M.A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, K. Eilbeck, S. Lewis, B. Marshall, C. Mungall, J. Richter, G.M. Rubin, J.A. Blake, C. Bult, M. Dolan, H. Drabkin, J.T. Eppig, D.P. Hill, L. Ni, M. Ringwald, R. Balakrishnan, J.M. Cherry, K.R. Christie, M.C. Costanzo, S.S. Dwight, S. Engel, D.G. Fisk, J.E. Hirschman, E.L. Hong, R.S. Nash, A. Sethuraman, C.L. Theesfeld, D. Botstein, K. Dolinski, B. Feierbach, T. Berardini, S. Mundodi, S.Y. Rhee, R. Apweiler, D. Barrell, E. Camon, E. Dimmer, V. Lee, R. Chisholm, P. Gaudet, W. Kibbe, R. Kishore, E.M. Schwarz, P. Sternberg, M. Gwinn, L. Hannick, J. Wortman, M. Berriman, V. Wood, N. de la Cruz, P. Tonellato, P. Jaiswal, T. Seigfried, R. White, Gene Ontology Consortium: The gene ontology (GO) database and informatics resource, Nucleic Acids Res. 32(Database issue), D258–261 (2004)

19.47.

Y. Guan, C.L. Myers, R. Lu, I.R. Lemischka, C.J. Bult, O.G. Troyanskaya: A genomewide functional network for the laboratory mouse, PLoS Comput. Biol. 4(9), e1000165 (2008)MathSciNetCrossRef

19.48.

T. Shlomi, D. Segal, E. Ruppin, R. Sharan: QPath: A method for querying pathways in a protein-protein interaction network, BMC Bioinformatics 7, 199 (2006)CrossRef

19.49.

I. Lee, S.V. Date, A.T. Adai, E.M. Marcotte: A probabilistic functional network of yeast genes, Science 306(5701), 1555–1558 (2004)CrossRef

19.50.

I. Lee, Z. Li, E.M. Marcotte: An improved, bias-reduced probabilistic functional gene network of bakerʼs yeast, Saccharomyces cerevisiae, PLoS One 2(10), e988 (2007)CrossRef

19.51.

I. Lee, B. Lehner, C. Crombie, W. Wong, A.G. Fraser, E.M. Marcotte: A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans, Nat. Genet. 40(2), 181–188 (2008)CrossRef

19.52.

I. Lee, B. Ambaru, P. Thakkar, E.M. Marcotte, S.Y. Rhee: Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, Nat. Biotechnol. 28(2), 149–156 (2010)CrossRef

19.53.

B. Linghu, E.S. Snitkin, Z. Hu, Y. Xia, C. Delisi: Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network, Genome Biol. 10(9), R91 (2009)CrossRef

19.54.

I. Lee, U.M. Blom, P.I. Wang, J.E. Shim, E.M. Marcotte: Prioritizing candidate disease genes by network-based boosting of genome-wide association data, Genome Res. 21(7), 1109–1121 (2011)CrossRef

19.55.

J. Scott, T. Ideker, R.M. Karp, R. Sharan: Efficient algorithms for detecting signaling pathways in protein interaction networks, J. Comput. Biol. 13(2), 133–144 (2006)MathSciNetCrossRefMATH

19.56.

G. Bebek, J. Yang: PathFinder: Mining signal transduction pathway segments from protein-protein interaction networks, BMC Bioinformatics 8, 335 (2007)CrossRef

19.57.

O. Ourfali, T. Shlomi, T. Ideker, E. Ruppin, R. Sharan: SPINE: A framework for signaling-regulatory pathway inference from cause-effect experiments, Bioinformatics 23(13), i359–366 (2007)CrossRef

19.58.

N. Yosef, L. Ungar, E. Zalckvar, A. Kimchi, M. Kupiec, E. Ruppin, R. Sharan: Toward accurate reconstruction of functional protein networks, Mol. Syst. Biol. 5, 248 (2009)CrossRef

19.59.

O. Vanunu, O. Magger, E. Ruppin, T. Shlomi, R. Sharan: Associating genes and protein complexes with disease via network propagation, PLoS Comput. Biol. 6(1), e1000641 (2010)MathSciNetCrossRef

19.60.

Y. Qi, Z. Bar-Joseph, J. Klein-Seetharaman: Evaluation of different biological data and computational classification methods for use in protein interaction prediction, Proteins 63(3), 490–500 (2006)CrossRef

19.61.

S. Suthram, T. Shlomi, E. Ruppin, R. Sharan, T. Ideker: A direct comparison of protein interaction confidence assignment schemes, BMC Bioinformatics 7, 360 (2006)CrossRef

19.62.

Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph: Random forest similarity for protein-protein interaction prediction from multiple sources, Pac. Symp. Biocomput. (2005) pp. 531–542

19.63.

X. Zhu, M. Gerstein, M. Snyder: Getting connected: Analysis and principles of biological networks, Genes Dev. 21(9), 1010–1024 (2007)CrossRef

19.64.

E. Yeger-Lotem, L. Riva, L.J. Su, A.D. Gitler, A.G. Cashikar, O.D. King, P.K. Auluck, M.L. Geddie, J.S. Valastyan, D.R. Karger, S. Lindquist, E. Fraenkel: Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity, Nat. Genet. 41(3), 316–323 (2009)CrossRef

19.65.

E. Cerami, E. Demir, N. Schultz, B.S. Taylor, C. Sander: Automated network analysis identifies core pathways in glioblastoma, PLoS One 5(2), e8918 (2010)CrossRef

19.66.

J. Bellay, G. Atluri, T.L. Sing, K. Toufighi, M. Costanzo, P.S. Ribeiro, G. Pandey, J. Baller, B. VanderSluis, M. Michaut, S. Han, P. Kim, G.W. Brown, B.J. Andrews, C. Boone, V. Kumar, C.L. Myers: Putting genetic interactions in context through a global modular decomposition, Genome Res. 21(8), 1375–1387 (2011)CrossRef

19.67.

C.Y. Huang, E. Fraenkel: Integration of proteomic, transcriptional, and interactome data reveals hidden signaling components, Sci. Signal. 2, ra40 (2009)

19.68.

X.M. Zhao, R.S. Wang, L. Chen, K. Aihara: Uncovering signal transduction networks from high-throughput data by integer linear programming, Nucleic Acids Res. 36(9), e48 (2008)CrossRef

19.69.

S. Lu, F. Zhang, J. Chen, S. Sze: Finding pathway structures in protein interaction networks, Algorithmica 48, 363–374 (2007)MathSciNetCrossRefMATH

19.70.

X. Ren, X. Zhou, L.Y. Wu, X.S. Zhang: An information-flow-based model with dissipation, saturation and direction for active pathway inference, BMC Syst. Biol. 4, 72 (2010)CrossRef

19.71.

M. Steffen, A. Petti, J. Aach, P. DʼHaeseleer, G. Church: Automated modelling of signal transduction networks, BMC Bioinformatics 3, 34 (2002)CrossRef

19.72.

A. Joshi, T. Van Parys, Y.V. Peer, T. Michoel: Characterizing regulatory path motifs in integrated networks using perturbational data, Genome Biol. 11(3), R32 (2010)CrossRef

19.73.

J. Pey, J. Prada, J.E. Beasley, F.J. Planes: Path finding methods accounting for stoichiometry in metabolic networks, Genome Biol. 12(5), R49 (2011)CrossRef

19.74.

N. Novershtern, A. Regev, N. Friedman: Physical Module Networks: An integrative approach for reconstructing transcription regulation, Bioinformatics 27(13), i177–i185 (2011)CrossRef

19.75.

Z. Hu, P.J. Killion, V.R. Iyer: Genetic reconstruction of a functional transcriptional regulatory network, Nat. Genet. 39(5), 683–687 (2007)CrossRef

19.76.

G. Chua, Q.D. Morris, R. Sopko, M.D. Robinson, O. Ryan, E.T. Chan, B.J. Frey, B.J. Andrews, C. Boone, T.R. Hughes: Identifying transcription factor functions and targets by phenotypic activation, Proc. Natl. Acad. Sci. USA 103(32), 12045–12050 (2006)CrossRef

19.77.

S.S. Shen-Orr, R. Milo, S. Mangan, U. Alon: Network motifs in the transcriptional regulation network of Escherichia coli, Nat. Genet. 31(1), 64–68 (2002)CrossRef

19.78.

L.V. Zhang, O.D. King, S.L. Wong, D.S. Goldberg, A.H. Tong, G. Lesage, B. Andrews, H. Bussey, C. Boone, F.P. Roth: Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network, J. Biol. 4(2), 6 (2005)

19.79.

N.M. Luscombe, M.M. Babu, H. Yu, M. Snyder, S.A. Teichmann, M. Gerstein: Genomic analysis of regulatory network dynamics reveals large topological changes, Nature 431(7006), 308–312 (2004)CrossRef

19.80.

C.H. Yeang, T. Ideker, T. Jaakkola: Physical network models, J. Comput. Biol. 11(2/3), 243–262 (2004)CrossRef

19.81.

C.H. Yeang, M. Vingron: A joint model of regulatory and metabolic networks, BMC Bioinformatics 7, 332 (2006)CrossRef

19.82.

A. Medvedovsky, V. Bafna, U. Zwick, R. Sharan: An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks, LNCS 5251, 222–232 (2008)MathSciNet

19.83.

A. Gitter, J. Klein-Seetharaman, A. Gupta, Z. Bar-Joseph: Discovering pathways by orienting edges in protein interaction networks, Nucleic Acids Res. 39(4), e22 (2011)CrossRef

19.84.

T.R. Hughes, M.J. Marton, A.R. Jones, C.J. Roberts, R. Stoughton, C.D. Armour, H.A. Bennett, E. Coffey, H. Dai, Y.D. He, M.J. Kidd, A.M. King, M.R. Meyer, D. Slade, P.Y. Lum, S.B. Stepaniants, D.D. Shoemaker, D. Gachotte, K. Chakraburtty, J. Simon, M. Bard, S.H. Friend: Functional discovery via a compendium of expression profiles, Cell 102(1), 109–126 (2000)CrossRef

19.85.

Y. Gilad, S.A. Rifkin, J.K. Pritchard: Revealing the architecture of gene regulation: The promise of eQTL studies, Trends Genet. 24(8), 408–415 (2008)CrossRef

19.86.

S. Suthram, A. Beyer, R.M. Karp, Y. Eldar, T. Ideker: eQED: An efficient method for interpreting eQTL associations using protein networks, Mol. Syst. Biol. 4, 162 (2008)CrossRef

19.87.

Z. Tu, L. Wang, M.N. Arbeitman, T. Chen, F. Sun: An integrative approach for causal gene identification and gene regulatory pathway inference, Bioinformatics 22(14), e489–496 (2006)CrossRef

19.88.

R.B. Brem, G. Yvert, R. Clinton, L. Kruglyak: Genetic dissection of transcriptional regulation in budding yeast, Science 296(5568), 752–755 (2002)CrossRef

19.89.

G. Yvert, R.B. Brem, J. Whittle, J.M. Akey, E. Foss, E.N. Smith, R. Mackelprang, L. Kruglyak: Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors, Nat. Genet. 35(1), 57–64 (2003)CrossRef

19.90.

Y.A. Kim, S. Wuchty, T.M. Przytycka: Identifying causal genes and dysregulated pathways in complex diseases, PLoS Comput. Biol. 7(3), e1001095 (2011)CrossRef

19.91.

J. Amberger, C.A. Bocchini, A.F. Scott, A. Hamosh: McKusickʼs online Mendelian inheritance in man (OMIM), Nucleic Acids Res. 37(Database issue), D793–796 (2009)CrossRef

19.92.

M. Oti, H.G. Brunner: The modular nature of genetic diseases, Clin. Genet. 71(1), 1–11 (2007)CrossRef

19.93.

M. Oti, B. Snel, M.A. Huynen, H.G. Brunner: Predicting disease genes using protein-protein interactions, J. Med. Genet. 43(8), 691–698 (2006)CrossRef

19.94.

R.A. George, J.Y. Liu, L.L. Feng, R.J. Bryson-Richardson, D. Fatkin, M.A. Wouters: Analysis of protein sequence and interaction data for candidate disease gene prediction, Nucleic Acids Res. 34(19), e130 (2006)CrossRef

19.95.

S. Kohler, S. Bauer, D. Horn, P.N. Robinson: Walking the interactome for prioritization of candidate disease genes, Am. J. Hum. Genet. 82(4), 949–958 (2008)CrossRef

19.96.

Y. Li, J.C. Patra: Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network, Bioinformatics 26(9), 1219–1224 (2010)CrossRef

19.97.

P. Yang, X. Li, M. Wu, C.K. Kwoh, S.K. Ng: Inferring gene-phenotype associations via global protein complex network propagation, PLoS One 6(7), e21502 (2011)CrossRef

19.98.

D. Nitsch, L.C. Tranchevent, B. Thienpont, L. Thorrez, H. Van Esch, K. Devriendt, Y. Moreau: Network analysis of differential expression for the identification of disease-causing genes, PLoS One 4(5), e5526 (2009)CrossRef

19.99.

C. Boone, H. Bussey, B.J. Andrews: Exploring genetic interactions and networks with yeast, Nat. Rev. Genet. 8(6), 437–449 (2007)CrossRef

19.100.

M. Cortón, J.I. Botella-Carretero, A. Benguria, G. Villuendas, A. Zaballos, J.L. San Millan, H.F. Escobar-Morreale, B. Peral: Differential gene expression profile in omental adipose tissue in women with polycystic ovary syndrome, J. Clin. Endocrinol. Metab. 92(1), 328–337 (2007)CrossRef

Titel: Path Finding in Biological Networks
verfasst von: Lore Cloots
Dries De Maeyer
Kathleen Marchal
Verlag: Springer Berlin Heidelberg
Buch: Springer Handbook of Bio-/Neuroinformatics
Print ISBN: 978-3-642-30573-3

Electronic ISBN: 978-3-642-30574-0

Copyright-Jahr: 2014
DOI: https://doi.org/10.1007/978-3-642-30574-0_19

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