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Network integration and graph analysis in mammalian molecular systems biology

Network integration and graph analysis in mammalian molecular systems biology

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Abstraction of intracellular biomolecular interactions into networks is useful for data integration and graph analysis. Network analysis tools facilitate predictions of novel functions for proteins, prediction of functional interactions and identification of intracellular modules. These efforts are linked with drug and phenotype data to accelerate drug-target and biomarker discovery. This review highlights the currently available varieties of mammalian biomolecular networks, and surveys methods and tools to construct, compare, integrate, visualise and analyse such networks.

Inspec keywords: drugs; graph theory; data mining; medical computing; cellular biophysics; molecular biophysics; proteins

Other keywords: network analysis tools; intracellular modules; intracellular biomolecular interactions; data mining; mammalian molecular systems biology; graph analysis; network integration; data standards; drug-target discovery; data integration; biomarker discovery

Subjects: Data handling techniques; Biology and medical computing; Combinatorial mathematics

References

    1. 1)
      • C.E. Horak , M.C. Mahajan , N.M. Luscombe , M. Gerstein , S.M. Weissman , M. Snyder . GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp–chip analysis. PNAS , 5 , 2924 - 2929
    2. 2)
      • A. Ma'ayan , S.L. Jenkins , S. Neves . Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science , 5737 , 1078 - 1083
    3. 3)
      • S. Zhong , K.F. Storch , O. Lipan , M.C. Kao , C.J. Weitz , W.H. Wong . GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in gene ontology space. Appl. Bioinf. , 4 , 261 - 264
    4. 4)
      • A. Ma'ayan , R.D. Blitzer , R. Iyengar . Toward predictive models of mammalian cells. Ann. Rev. Biophys. Biomol. Struct. , 1 , 319 - 349
    5. 5)
      • J. Lee , G. Katari , R. Sachidanandam . GObar: a gene ontology based analysis and visualization tool for gene sets. BMC Bioinf. , 1
    6. 6)
      • H. Hermjakob , L. Montecchi-Palazzi , C. Lewington . IntAct: an open source molecular interaction database. Nucl. Acids Res. , D452 - D455
    7. 7)
      • J. Yoon , A. Blumer , K. Lee . An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality. Bioinformatics , 24 , 3106 - 3108
    8. 8)
      • C. Pasquier , F. Girardot , K. Jevardat de Fombelle , R. Christen . THEA: ontology-driven analysis of microarray data. Bioinformatics , 16 , 2636 - 2643
    9. 9)
      • P. Shannon , D. Reiss , R. Bonneau , N. Baliga . The gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinf. , 1
    10. 10)
      • C.M. Lloyd , M.D. Halstead , P.F. Nielsen . CellML: its future, present and past. Prog. Biophys. Mol. Biol. , 433 - 450
    11. 11)
      • H. Ogata , S. Goto , K. Sato , W. Fujibuchi , H. Bono , M. Kanehisa . KEGG: Kyoto encyclopedia of genes and genomes. Nucl. Acids Res. , 1 , 29 - 34
    12. 12)
      • G. Joshi-Tope , M. Gillespie , I. Vastrik . Reactome: a knowledge base of biological pathways. Nucl. Acids Res. , D428 - D432
    13. 13)
      • N.A. Kolchanov , O.A. Podkolodnaya , E.A. Ananko . Transcription regulatory regions database (TRRD): its status in 2000. Nucl. Acids Res. , 1 , 298 - 301
    14. 14)
      • H.N. Chua , W.-K. Sung , L. Wong . Exploiting indirect neighbours and topological weight to predict protein function from protein–protein interactions. Bioinformatics , 13 , 1623 - 1630
    15. 15)
      • X. Zhu , M. Gerstein , M. Snyder . Getting connected: analysis and principles of biological networks. Genes Dev. , 9 , 1010 - 1024
    16. 16)
      • A.J. Frodsham , J.P. Higgins . Online genetic databases informing human genome epidemiology. BMC Med. Res. Methodol.
    17. 17)
      • S.S. Shen-Orr , R. Milo , S. Mangan , U. Alon . Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. , 1 , 64 - 68
    18. 18)
      • S.I. Berger , R. Iyengar , A. Ma'ayan . AVIS: AJAX viewer of interactive signaling networks. Bioinformatics , 20 , 2803 - 2805
    19. 19)
      • M.J. Herrgard , S.S. Fong , B. Palsson . Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput. Biol. , 7
    20. 20)
      • T. Handorf , O. Ebenhoh . MetaPath online: a web server implementation of the network expansion algorithm. Nucl. Acids Res. , W613 - W618
    21. 21)
      • N.R. Gough . Science's signal transduction knowledge environment: the connections maps database. Ann. NY Acad. Sci. , 585 - 587
    22. 22)
      • Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature , 7145 , 661 - 678
    23. 23)
      • F. Luo , Y. Yang , C.-F. Chen , R. Chang , J. Zhou , R.H. Scheuermann . Modular organization of protein interaction networks. Bioinformatics , 2 , 207 - 214
    24. 24)
      • B.P. Kelley , B. Yuan , F. Lewitter , R. Sharan , B.R. Stockwell , T. Ideker . PathBLAST: a tool for alignment of protein interaction networks. Nucl. Acids Res. , W83 - W88
    25. 25)
      • M. Kanehisa , S. Goto . KEGG: Kyoto encyclopedia of genes and genomes. Nucl. Acids Res. , 1 , 27 - 30
    26. 26)
      • R. Shalgi , D. Lieber , M. Oren , Y. Pilpel . Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol. , 7
    27. 27)
      • G.W. Flake , S. Lawrence , C.L. Giles , F.M. Coetzee . Self-organization and identification of web communities. Computer , 3 , 66 - 70
    28. 28)
      • U. Dogrusoz , E.Z. Erson , E. Giral . PATIKAweb: a web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics , 3 , 374 - 375
    29. 29)
      • C. Gene Ontology . The gene ontology (GO) database and informatics resource. Nucl. Acids Res. , D258 - D261
    30. 30)
      • E.I. Boyle , S. Weng , J. Gollub . GO::TermFinder – open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics , 18 , 3710 - 3715
    31. 31)
      • G. Chaurasia , Y. Iqbal , C. Hanig , H. Herzel , E.E. Wanker , M.E. Futschik . UniHI: an entry gate to the human protein interactome. Nucl. Acids Res. , D590 - D594
    32. 32)
      • S. Takamori , M. Holt , K. Stenius . Molecular anatomy of a trafficking organelle. Cell , 4 , 831 - 846
    33. 33)
      • A. Zanzoni , L. Montecchi-Palazzi , M. Quondam , G. Ausiello , M. Helmer-Citterich , G. Cesareni . MINT: a molecular INTeraction database. FEBS Lett. , 1 , 135 - 140
    34. 34)
      • E. Cerami , G. Bader , B. Gross , C. Sander . cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinf. , 1
    35. 35)
      • A. Yuryev , Z. Mulyukov , E. Kotelnikova . Automatic pathway building in biological association networks. BMC Bioinf. , 1
    36. 36)
      • R. Hoffmann , A. Valencia . Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics , ii252 - ii258
    37. 37)
      • C. Stark , B.-J. Breitkreutz , T. Reguly , L. Boucher , A. Breitkreutz , M. Tyers . BioGRID: a general repository for interaction datasets. Nucl. Acids Res. , D535 - D539
    38. 38)
      • H. Liu , Z.-Z. Hu , C. Wu . DynGO: a tool for visualizing and mining of gene ontology and its associations. BMC Bioinf. , 1
    39. 39)
      • T.-W. Huang , A.-C. Tien , W.-S. Huang . POINT: a database for the prediction of protein–protein interactions based on the orthologous interactome. Bioinformatics , 17 , 3273 - 3276
    40. 40)
      • N. Przulj , D.G. Corneil , I. Jurisica . Efficient estimation of graphlet frequency distributions in protein–protein interaction networks. Bioinformatics , 8 , 974 - 980
    41. 41)
      • P.M. Roberts . Mining literature for systems biology. Brief Bioinf. , 4 , 399 - 406
    42. 42)
      • K. Han , B. Park , H. Kim , J. Hong , J. Park . HPID: the human protein interaction database. Bioinformatics , 15 , 2466 - 2470
    43. 43)
      • C. von Mering , R. Krause , B. Snel . Comparative assessment of large-scale data sets of protein–protein interactions. Nature , 6887 , 399 - 403
    44. 44)
      • C.J. Krieger , P. Zhang , L.A. Mueller . MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucl. Acids Res. , D438 - D442
    45. 45)
      • S.M. Keating , B.J. Bornstein , A. Finney , M. Hucka . SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics , 10 , 1275 - 1277
    46. 46)
      • White, A.G., Ma'ayan, A.: `Connecting seed lists of mammalian proteins using Steiner trees', ACSSC 2007. Conf. Record of the 41st Asilomar Conf. Signals, Systems and Computers, 4–7 November 2007, Pacific Grove, CA, USA, p. 155–159.
    47. 47)
      • R. Linding , L.J. Jensen , G.J. Ostheimer . Systematic discovery of in vivo phosphorylation networks. Cell , 7 , 1415 - 1426
    48. 48)
      • T. Beissbarth , T.P. Speed . GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics , 9 , 1464 - 1465
    49. 49)
      • M.P. Cary , G.D. Bader , C. Sander . Pathway information for systems biology. FEBS Lett. , 8 , 1815 - 1820
    50. 50)
      • L. Salwinski , C.S. Miller , A.J. Smith , F.K. Pettit , J.U. Bowie , D. Eisenberg . The database of interacting proteins: 2004 update. Nucl. Acids Res. , D449 - D451
    51. 51)
      • J. Zhu , M.Q. Zhang . SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics , 7 , 607 - 611
    52. 52)
      • J. Chen , B. Yuan . Detecting functional modules in the yeast protein–protein interaction network. Bioinformatics , 18 , 2283 - 2290
    53. 53)
      • P. Shannon , A. Markiel , O. Ozier . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. , 11 , 2498 - 2504
    54. 54)
      • A. Tanay , R. Sharan , M. Kupiec , R. Shamir . Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. PNAS , 9 , 2981 - 2986
    55. 55)
      • M. Krummenacker , S. Paley , L. Mueller , T. Yan , P.D. Karp . Querying and computing with BioCyc databases. Bioinformatics , 16 , 3454 - 3455
    56. 56)
      • G. Chaurasia , H. Herzel , E.E. Wanker , M.E. Futschik . Systematic functional assessment of human protein–protein interaction maps. Genome Inf. , 1 , 36 - 45
    57. 57)
      • T. Lee , Y. Pouliot , V. Wagner . BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinf. , 1
    58. 58)
      • M.S. Scott , T. Perkins , S. Bunnell , F. Pepin , D.Y. Thomas , M. Hallett . Identifying regulatory subnetworks for a set of genes. Mol. Cell Proteomics , 5 , 683 - 692
    59. 59)
      • Z. Lubovac , J. Gamalielsson , B. Olsson . Combining functional and topological properties to identify core modules in protein interaction networks. Proteins , 4 , 948 - 959
    60. 60)
      • M.A. Yildirim , K.-I. Goh , M.E. Cusick , A.-L. Barabasi , M. Vidal . Drug target network. Nat. Biotech. , 10 , 1119 - 1126
    61. 61)
      • P.M. Kim , L.J. Lu , Y. Xia , M.B. Gerstein . Relating three-dimensional structures to protein networks provides evolutionary insights. Science , 5807 , 1938 - 1941
    62. 62)
      • B. Settles . ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics , 14 , 3191 - 3192
    63. 63)
      • R. Milo , S. Itzkovitz , N. Kashtan . Superfamilies of evolved and designed networks. Science , 5663 , 1538 - 1542
    64. 64)
      • K. Lage , E.O. Karlberg , Z.M. Storling . A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat. Biotech. , 3 , 309 - 316
    65. 65)
      • G. Dennis , B. Sherman , D. Hosack . DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. , 5
    66. 66)
      • M. Krallinger , A. Valencia . Text-mining and information-retrieval services for molecular biology. Genome Biol. , 7
    67. 67)
      • J.M. Fernandez , R. Hoffmann , A. Valencia . iHOP web services. Nucl. Acids Res. , W21 - W26
    68. 68)
      • R. Albert . Scale-free networks in cell biology. J. Cell Sci. , 21 , 4947 - 4957
    69. 69)
      • V. Marinescu , I. Kohane , A. Riva . MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinf. , 1
    70. 70)
      • N. Goffard , G. Weiller . PathExpress: a web-based tool to identify relevant pathways in gene expression data. Nucl. Acids Res. , W176 - W181
    71. 71)
      • C. The UniProt . The universal protein resource (UniProt). Nucl. Acids Res. , D193 - D197
    72. 72)
      • G.R. Mishra , M. Suresh , K. Kumaran . Human protein reference database–2006 update. Nucl. Acids Res. , D411 - D414
    73. 73)
      • P. Kersey , R. Apweiler . Linking publication, gene and protein data. Nat. Cell Biol. , 11 , 1183 - 1189
    74. 74)
      • A.R. Joyce , B.O. Palsson . The model organism as a system: integrating ‘omics’ data sets. Nat. Rev. Mol. Cell Biol. , 3 , 198 - 210
    75. 75)
      • J. Forster , I. Famili , P. Fu , B.O. Palsson , J. Nielsen . Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. , 244 - 253
    76. 76)
      • C. von Mering , L.J. Jensen , M. Kuhn . STRING 7 – recent developments in the integration and prediction of protein interactions. Nucl. Acids Res. , D358 - D362
    77. 77)
      • R. Albert . Network inference, analysis, and modeling in systems biology. Plant Cell , 11 , 3327 - 3338
    78. 78)
      • G. Robertson , M. Hirst , M. Bainbridge . Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Meth. , 8 , 651 - 657
    79. 79)
      • C. Plake , T. Schiemann , M. Pankalla , J. Hakenberg , U. Leser . ALIBABA: PubMed as a graph. Bioinformatics , 19 , 2444 - 2445
    80. 80)
      • S. Kerrien , Y. Alam-Faruque , B. Aranda . IntAct – open source resource for molecular interaction data. Nucl. Acids Res. , D561 - D565
    81. 81)
      • I. Albert , R. Albert . Conserved network motifs allow protein–protein interaction prediction. Bioinformatics , 18 , 3346 - 3352
    82. 82)
      • G. Ruvkun . Molecular biology: glimpses of a tiny RNA world. Science , 5543 , 797 - 799
    83. 83)
      • D. Hosack , G. Dennis , B. Sherman , H. Lane , R. Lempicki . Identifying biological themes within lists of genes with EASE. Genome Biol. , 10
    84. 84)
      • M. Holford , N. Li , P. Nadkarni , H. Zhao . VitaPad: visualization tools for the analysis of pathway data. Bioinformatics , 8 , 1596 - 1602
    85. 85)
      • W3C Extensible Markup Language (XML) [http://www.w3.org/XML/].
    86. 86)
      • M. Hucka , A. Finney , H.M. Sauro . The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics , 4 , 524 - 531
    87. 87)
      • A. Conesa , S. Gotz , J.M. Garcia-Gomez , J. Terol , M. Talon , M. Robles . Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics , 18 , 3674 - 3676
    88. 88)
      • A. Ludemann , D. Weicht , J. Selbig , J. Kopka . PaVESy: pathway visualization and editing system. Bioinformatics , 16 , 2841 - 2844
    89. 89)
      • Z. Hu , J. Mellor , J. Wu , T. Yamada , D. Holloway . DeLisi C: VisANT: data-integrating visual framework for biological networks and modules. Nucl. Acids Res. , W352 - W357
    90. 90)
      • S.A. Racunas , N.H. Shah , I. Albert , N.V. Fedoroff . HyBrow: a prototype system for computer-aided hypothesis evaluation. Bioinformatics , i257 - i264
    91. 91)
      • J.M. Cherry , C. Adler , C. Ball . SGD: Saccharomyces genome database. Nucl. Acids Res. , 1 , 73 - 79
    92. 92)
      • C. Klukas , F. Schreiber . Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics , 3 , 344 - 350
    93. 93)
      • S. Asthana , O.D. King , F.D. Gibbons , F.P. Roth . Predicting protein complex membership using probabilistic network reliability. Genome Res. , 6 , 1170 - 1175
    94. 94)
      • G.W. Carter . Inferring network interactions within a cell. Brief Bioinf. , 4 , 380 - 389
    95. 95)
      • G.F. Cooper , E. Herskovits . A Bayesian method for the induction of probabilistic networks from data. Mach. Learn. , 309 - 347
    96. 96)
      • P.J. Woolf , W. Prudhomme , L. Daheron , G.Q. Daley , D.A. Lauffenburger . Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. Bioinformatics , 6 , 741 - 753
    97. 97)
      • M. Pachkov , I. Erb , N. Molina , E. van Nimwegen . SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucl. Acids Res. , D127 - D131
    98. 98)
      • M. Koyuturk , Y. Kim , U. Topkara , S. Subramaniam , W. Szpankowski , A. Grama . Pairwise alignment of protein interaction networks. J. Comput. Biol. , 2 , 182 - 199
    99. 99)
      • S. Peri , J.D. Navarro , R. Amanchy . Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. , 10 , 2363 - 2371
    100. 100)
      • M.E.J. Newman . Scientific collaboration networks. Part II. Shortest paths, weighted networks, and centrality. Phys. Rev. E , 1
    101. 101)
      • K. Sachs , O. Perez , D. Pe'er , D.A. Lauffenburger , G.P. Nolan . Causal protein-signaling networks derived from multiparameter single-cell data. Science , 5721 , 523 - 529
    102. 102)
      • Z. Li , S. Zhang , Y. Wang , X.-S. Zhang , L. Chen . Alignment of molecular networks by integer quadratic programming. Bioinformatics , 13 , 1631 - 1639
    103. 103)
      • A. Ma'ayan , S.L. Jenkins , J. Goldfarb , R. Iyengar . Network analysis of FDA approved drugs and their targets. Mount Sinai J. Med. A, J. Transl. Pers. Med. , 1 , 27 - 32
    104. 104)
      • O. Garcia , C. Saveanu , M. Cline . GOlorize: a Cytoscape plug-in for network visualization with gene ontology-based layout and coloring. Bioinformatics , 3 , 394 - 396
    105. 105)
      • A. Lipshtat , S.P. Purushothaman , R. Iyengar , A. Ma'ayan . Functions of bifans in context of multiple regulatory motifs in signaling networks. Biophys. J. , 7 , 2566 - 2579
    106. 106)
      • A. Chang , J. McDermott , Z. Frazier , M. Guerquin , R. Samudrala . INTEGRATOR: interactive graphical search of large protein interactomes over the web. BMC Bioinf. , 1
    107. 107)
      • S. Letovsky , S. Kasif . Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics , i197 - i204
    108. 108)
      • A. Nikitin , S. Egorov , N. Daraselia , I. Mazo . Pathway studio – the analysis and navigation of molecular networks. Bioinformatics , 16 , 2155 - 2157
    109. 109)
      • A. Ma'ayan , R. Iyengar . From components to regulatory motifs in signalling networks. Brief Funct. Genomic Proteomic , 1 , 57 - 61
    110. 110)
      • M.E.J. Newman . From the cover: modularity and community structure in networks. PNAS , 23 , 8577 - 8582
    111. 111)
      • M. Kellis , N. Patterson , M. Endrizzi , B. Birren , E.S. Lander . Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature , 6937 , 241 - 254
    112. 112)
      • B.J. Frey , D. Dueck . Clustering by passing messages between data points. Science , 5814 , 972 - 976
    113. 113)
      • P.D. Karp , M. Riley , S.M. Paley , A. Pellegrini-Toole . The MetaCyc database. Nucl. Acids Res. , 1 , 59 - 61
    114. 114)
      • K.R. Christie , S. Weng , R. Balakrishnan . Saccharomyces genome database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucl. Acids Res. , D311 - D314
    115. 115)
      • Z. Liang , M. Xu , M. Teng , L. Niu . Comparison of protein interaction networks reveals species conservation and divergence. BMC Bioinf. , 1
    116. 116)
      • D. Nam , S.-B. Kim , S.-K. Kim , S. Yang , S.-Y. Kim , I.-S. Chu . ADGO: analysis of differentially expressed gene sets using composite GO annotation. Bioinformatics , 18 , 2249 - 2253
    117. 117)
      • A.M. Cohen , W.R. Hersh , C. Dubay , K. Spackman . Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts. BMC Bioinf. , 1
    118. 118)
      • J. Xu , Y. Li . Discovering disease-genes by topological features in human protein–protein interaction network. Bioinformatics , 22 , 2800 - 2805
    119. 119)
      • M.J. Schuemie , B. Mons , M. Weeber , J.A. Kors . Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. J. Biomed. Inf. , 3 , 316 - 324
    120. 120)
      • L. Hood , J.R. Heath , M.E. Phelps , B. Lin . Systems biology and new technologies enable predictive and preventative medicine. Science , 5696 , 640 - 643
    121. 121)
      • M. Deng , K. Zhang , S. Mehta , T. Chen , F. Sun . Prediction of protein function using protein–protein interaction data. J. Comput. Biol. , 947 - 960
    122. 122)
      • S. Gong , G. Yoon , I. Jang . PSIbase: a database of protein structural interactome map (PSIMAP). Bioinformatics , 10 , 2541 - 2543
    123. 123)
      • V. Spirin , L.A. Mirny . Protein complexes and functional modules in molecular networks. PNAS , 21 , 12123 - 12128
    124. 124)
      • Y. Tsuruoka , J.I. Tsujii . Improving the performance of dictionary-based approaches in protein name recognition. J. Biomed. Inf. , 6 , 461 - 470
    125. 125)
      • Z. Hu , D.M. Ng , T. Yamada . VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucl. Acids Res. , W625 - W632
    126. 126)
      • R. Caspi , H. Foerster , C.A. Fulcher . MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucl. Acids Res. , D511 - D516
    127. 127)
      • F. Radicchi , C. Castellano , F. Cecconi , V. Loreto , D. Parisi . Defining and identifying communities in networks. PNAS, USA , 9 , 2658 - 2663
    128. 128)
      • R. Sealfon , M. Hibbs , C. Huttenhower , C. Myers , O. Troyanskaya . GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinf. , 1
    129. 129)
      • A. Meil , P. Durand , J. Wojcik . PIMWalker: visualising protein interaction networks using the HUPO PSI molecular interaction format. Appl. Bioinf. , 2 , 137 - 139
    130. 130)
      • K.D. Bromberg , A. Ma'ayan , S.R. Neves , R. Iyengar . Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science , 5878 , 903 - 909
    131. 131)
      • H. Schmidt , M. Jirstrand . Systems biology toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics , 4 , 514 - 515
    132. 132)
      • V. Matys , O.V. Kel-Margoulis , E. Fricke . TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes. Nucl. Acids Res. , D108 - D110
    133. 133)
      • J.S. Edwards , B.O. Palsson . The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. PNAS , 10 , 5528 - 5533
    134. 134)
      • R. Apweiler , A. Bairoch , C.H. Wu . UniProt: the universal protein knowledgebase. Nucl. Acids Res. , D115 - D119
    135. 135)
      • A. Rzhetsky , I. Iossifov , T. Koike . GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Inf. , 1 , 43 - 53
    136. 136)
      • R. Sharan , I. Ulitsky , R. Shamir . Network-based prediction of protein function. Mol. Syst. Biol.
    137. 137)
      • K. Xia , D. Dong , J.-D. Han . IntNetDB v1.0: an integrated protein–protein interaction network database generated by a probabilistic model. BMC Bioinf. , 1
    138. 138)
      • G. Bader , C. Hogue . An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinf. , 1
    139. 139)
      • A. Funahashi , N. Tanimura , M. Morohashi , H. Kitano . CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO , 159 - 162
    140. 140)
      • M.C. Teixeira , P. Monteiro , P. Jain . The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucl. Acids Res. , D446 - D451
    141. 141)
      • R. Hoffmann , M. Krallinger , E. Andres , J. Tamames , C. Blaschke , A. Valencia . Text mining for metabolic pathways, signaling cascades, and protein networks. Sci. STKE , 283
    142. 142)
      • A. Birkland , G. Yona . BIOZON: a system for unification, management and analysis of heterogeneous biological data. BMC Bioinf. , 1
    143. 143)
      • A. Skusa , A. Ruegg , J. Kohler . Extraction of biological interaction networks from scientific literature. Brief Bioinf. , 3 , 263 - 276
    144. 144)
      • N. Daraselia , A. Yuryev , S. Egorov , I. Mazo , I. Ispolatov . Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinf.
    145. 145)
      • D. Bu , Y. Zhao , L. Cai . Topological structure analysis of the protein–protein interaction network in budding yeast. Nucl. Acids Res. , 9 , 2443 - 2450
    146. 146)
      • N. Tran , C. Baral , V.J. Nagaraj , L. Joshi . Knowledge-based framework for hypothesis formation in biochemical networks. Bioinformatics , ii213 - ii219
    147. 147)
      • A. Chatr-aryamontri , A. Ceol , L.M. Palazzi . MINT: the molecular INTeraction database. Nucl. Acids Res. , D572 - D574
    148. 148)
      • G.D. Zhou . Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoid. Int. J. Med. Inf. , 6 , 456 - 467
    149. 149)
      • R. Feldman , J.S.C.U. Press . (2006) The text mining handbook.
    150. 150)
      • M. Girvan , M.E. Newman . Community structure in social and biological networks. PNAS, USA , 12 , 7821 - 7826
    151. 151)
      • K. Fundel , R. Zimmer . Gene and protein nomenclature in public databases. BMC Bioinf. , 1
    152. 152)
      • C.H. Busold , S. Winter , N. Hauser . Integration of GO annotations in correspondence analysis: facilitating the interpretation of microarray data. Bioinformatics , 10 , 2424 - 2429
    153. 153)
      • C.T. Harbison , D.B. Gordon , T.I. Lee . Transcriptional regulatory code of a eukaryotic genome. Nature , 7004 , 99 - 104
    154. 154)
      • A.W. Rives , T. Galitski . Modular organization of cellular networks. PNAS , 3 , 1128 - 1133
    155. 155)
      • H. Hishigaki , K. Nakai , T. Ono , A. Tanigami , T. Takagi . Assessment of prediction accuracy of protein function from protein–protein interaction data. Yeast , 6 , 523 - 531
    156. 156)
      • J. Ye , L. Fang , H. Zheng . WEGO: a web tool for plotting GO annotations. Nucl. Acids Res. , W293 - W297
    157. 157)
      • M. Ashburner , C.A. Ball , J.A. Blake . Gene ontology: tool for the unification of biology. Nat. Genet. , 1 , 25 - 29
    158. 158)
      • H. Yu , A. Paccanaro , V. Trifonov , M. Gerstein . Predicting interactions in protein networks by completing defective cliques. Bioinformatics , 7 , 823 - 829
    159. 159)
      • K.-I. Goh , M.E. Cusick , D. Valle , B. Childs , M. Vidal , A.-L. Barabasi . The human disease network. PNAS , 21 , 8685 - 8690
    160. 160)
      • M.A. van Driel , J. Bruggeman , G. Vriend , H.G. Brunner , J.A. Leunissen . A text-mining analysis of the human phenome. Eur. J. Hum. Genet. , 5 , 535 - 542
    161. 161)
      • S. Brohee , J. van Helden . Evaluation of clustering algorithms for protein–protein interaction networks. BMC Bioinf. , 1
    162. 162)
      • S.E. Dreyfus , R.A. Wagner . The Steiner problem in graphs. Networks
    163. 163)
      • S. Mathivanan , B. Periaswamy , T.K.B. Gandhi . An evaluation of human protein–protein interaction data in the public domain. BMC Bioinf.
    164. 164)
      • F. Diella , S. Cameron , C. Gemund . Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinf. , 1
    165. 165)
      • S. Berger , J. Posner , A. Ma'ayan . Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinf. , 1
    166. 166)
      • S. Orchard , H. Hermjakob , C.F. Taylor . Further steps in standardisation report of the second annual proteomics standards initiative spring workshop. PROTEOMICS , 14 , 3552 - 3555
    167. 167)
      • A.J. Enright , S. Van Dongen , C.A. Ouzounis . An efficient algorithm for large-scale detection of protein families. Nucl. Acids Res. , 7 , 1575 - 1584
    168. 168)
      • S. Shah , Y. Huang , T. Xu , M. Yuen , J. Ling , B.F.F. Ouellette . Atlas – a data warehouse for integrative bioinformatics. BMC Bioinf. , 1
    169. 169)
      • Page, L.B., Sergey Motwani, R., Winograd, T.: `The PageRank citation ranking: bringing order to the web', Stanford InfoLab Publication Server, 1998.
    170. 170)
      • I. Avila-Campillo , K. Drew , J. Lin , D.J. Reiss , R. Bonneau . BioNetBuilder: automatic integration of biological networks. Bioinformatics , 3 , 392 - 393
    171. 171)
      • H. Hackl , M. Maurer , B. Mlecnik . GOLD.db: genomics of lipid-associated disorders database. BMC Genomics , 1
    172. 172)
      • Z. Liang , M. Xu , M. Teng , L. Niu . NetAlign: a web-based tool for comparison of protein interaction networks. Bioinformatics , 17 , 2175 - 2177
    173. 173)
      • H.K. Tsai , M.Y. Chou , C.H. Shih , G.T. Huang , T.H. Chang , W.H. Li . MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucl. Acids Res. , W221 - W226
    174. 174)
      • L. Stromback , P. Lambrix . Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics , 24 , 4401 - 4407
    175. 175)
      • S. Peri , J.D. Navarro , T.Z. Kristiansen . Human protein reference database as a discovery resource for proteomics. Nucl. Acids Res. , D497 - D501
    176. 176)
      • Nature. Nature , 6968 , 789 - 796
    177. 177)
      • D. Endy . Foundations for engineering biology. Nature , 7067 , 449 - 453
    178. 178)
      • M.E. Futschik , G. Chaurasia , H. Herzel . Comparison of human protein–protein interaction maps. Bioinformatics , 5 , 605 - 611
    179. 179)
      • H. Hermjakob , L. Montecchi-Palazzi , G.C. Bader . The HUPO PSI's molecular interaction format – a community standard for the representation of protein interaction data. Nat. Biotech. , 2 , 177 - 183
    180. 180)
      • C.L. Freeman . A set of measures of centrality based on betweenness. Sociometry , 35 - 41
    181. 181)
      • L. Franke , H.V. Bakel , L. Fokkens , E.D. de Jong , M. Egmont-Petersen , C. Wijmenga . Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. , 6 , 1011 - 1025
    182. 182)
      • D. Martin , C. Brun , E. Remy , P. Mouren , D. Thieffry , B. Jacq . GOToolBox: functional analysis of gene datasets based on gene ontology. Genome Biol. , 12
    183. 183)
      • A haplotype map of the human genome. Nature , 7063 , 1299 - 1320
    184. 184)
      • P. Beltrao , C. Kiel , L. Serrano . Structures in systems biology. Curr. Opin. Struct. Biol. , 3 , 378 - 384
    185. 185)
      • J.R. Swedlow , S.E. Lewis , I.G. Goldberg . Modelling data across labs, genomes, space and time. Nat. Cell Biol. , 11 , 1190 - 1194
    186. 186)
      • T. Sen , A. Kloczkowski , R. Jernigan . Functional clustering of yeast proteins from the protein–protein interaction network. BMC Bioinf. , 1
    187. 187)
      • B. Andreopoulos , A. An , X. Wang , M. Faloutsos , M. Schroeder . Clustering by common friends finds locally significant proteins mediating modules. Bioinformatics , 9 , 1124 - 1131
    188. 188)
      • G. Zhou , J. Zhang , J. Su , D. Shen , C. Tan . Recognizing names in biomedical texts: a machine learning approach. Bioinformatics , 7 , 1178 - 1190
    189. 189)
      • K. Webb , T. White . UML as a cell and biochemistry modeling language. Biosystems , 3 , 283 - 302
    190. 190)
      • H.S. Moon , J. Bhak , K.H. Lee , D. Lee . Architecture of basic building blocks in protein and domain structural interaction networks. Bioinformatics , 8 , 1479 - 1486
    191. 191)
      • J. Morrison , R. Breitling , D. Higham , D. Gilbert . GeneRank: using search engine technology for the analysis of microarray experiments. BMC Bioinf. , 1
    192. 192)
      • B. Smith , W. Ceusters , B. Klagges . Relations in biomedical ontologies. Genome Biol. , 5
    193. 193)
      • K.R. Patil , J. Nielsen . Uncovering transcriptional regulation of metabolism by using metabolic network topology. PNAS , 8 , 2685 - 2689
    194. 194)
      • I.J. Grady Booch , J. Rumbaugh , I. Jacobson . (2005) The unified modeling language user guide.
    195. 195)
      • A. Birkland , G. Yona . BIOZON: a hub of heterogeneous biological data. Nucl. Acids Res. , D235 - D242
    196. 196)
      • N.A. Kolchanov , E.A. Ananko , O.A. Podkolodnaya . Transcription regulatory regions database (TRRD): its status in 1999. Nucl. Acids Res. , 1 , 303 - 306
    197. 197)
      • J.S. Edwards , R.U. Ibarra , B.O. Palsson . In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotech. , 2 , 125 - 130
    198. 198)
      • I. Xenarios , D.W. Rice , L. Salwinski , M.K. Baron , E.M. Marcotte , D. Eisenberg . DIP: the database of interacting proteins. Nucl. Acids Res. , 1 , 289 - 291
    199. 199)
      • Y. Tao , L. Sam , J. Li , C. Friedman , Y.A. Lussier . Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics , 13 , i529 - i538
    200. 200)
      • C.D. Bajdik , B. Kuo , S. Rusaw , S. Jones , A. Brooks-Wilson . CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes. BMC Bioinf. , 1
    201. 201)
      • O.V. Kel-Margoulis , A.E. Kel , I. Reuter , I.V. Deineko , E. Wingender . TRANSCompel(R): a database on composite regulatory elements in eukaryotic genes. Nucl. Acids Res. , 1 , 332 - 334
    202. 202)
      • L. Shi , F. Campagne . Building a protein name dictionary from full text: a machine learning term extraction approach. BMC Bioinf. , 1
    203. 203)
      • K.R. Brown , I. Jurisica . Online predicted human interaction database. Bioinformatics , 9 , 2076 - 2082
    204. 204)
      • S. Maere , K. Heymans , M. Kuiper . BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics , 16 , 3448 - 3449
    205. 205)
      • D.J. Watts , S.H. Strogatz . Collective dynamics of small-world networks. Nature , 6684 , 440 - 442
    206. 206)
      • S. Bornholdt . Systems biology. Less is more in modeling large genetic networks. Science , 5747 , 449 - 451
    207. 207)
      • L.H. Hartwell , J.J. Hopfield , S. Leibler , A.W. Murray . From molecular to modular cell biology. Nature , C47 - C52
    208. 208)
      • L.J. Lu , A. Sboner , Y.J. Huang . Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem. Sci. , 7 , 320 - 331
    209. 209)
      • S. Bandyopadhyay , R. Sharan , T. Ideker . Systematic identification of functional orthologs based on protein network comparison. Genome Res. , 3 , 428 - 435
    210. 210)
      • M.E. Newman . A measure of betweenness centrality based on random walks. Social Networks , 1 , 39 - 54
    211. 211)
      • R. Rubinstein , I. Simon . MILANO – custom annotation of microarray results using automatic literature searches. BMC Bioinf. , 1
    212. 212)
      • Q. Cui , Z. Yu , E.O. Purisima , E. Wang . Principles of microRNA regulation of a human cellular signaling network. Mol. Syst. Biol.
    213. 213)
      • T. Beuming , L. Skrabanek , M.Y. Niv , P. Mukherjee , H. Weinstein . PDZBase: a protein–protein interaction database for PDZ-domains. Bioinformatics , 6 , 827 - 828
    214. 214)
      • T.G.O. Consortium . Creating the gene ontology resource: design and implementation. Genome Res. , 8 , 1425 - 1433
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