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Madhusudan Natarajan, Keng-mean Lin, R. Hsueh, P. Sternweis, R. Ranganathan (2006)
A global analysis of cross-talk in a mammalian cellular signalling networkNature Cell Biology, 8
Pall Jonsson, P. Bates (2006)
Global topological features of cancer proteins in the human interactomeBioinformatics, 22 18
A. Kapp, S. Jeffrey, A. Langerød, A. Børresen-Dale, W. Han, D. Noh, I. Bukholm, Monica Nicolau, P. Brown, R. Tibshirani (2006)
Discovery and validation of breast cancer subtypesBMC Genomics, 7
K. Basso, Adam Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera, A. Califano (2005)
Reverse engineering of regulatory networks in human B cellsNature Genetics, 37
D. Tsafrir, M. Bacolod, Z. Selvanayagam, I. Tsafrir, J. Shia, Z. Zeng, Hao Liu, Curtis Krier, R. Stengel, F. Barany, W. Gerald, P. Paty, E. Domany, D. Notterman (2006)
Relationship of gene expression and chromosomal abnormalities in colorectal cancer.Cancer research, 66 4
S. Shen-Orr, R. Milo, S. Mangan, U. Alon (2002)
Network motifs in the transcriptional regulation network of Escherichia coliNature Genetics, 31
Ben Lehner, Catriona Crombie, Julia Tischler, A. Fortunato, A. Fraser (2006)
Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathwaysNature Genetics, 38
A. Lenferink, J. Magoon, C. Cantin, M. O’Connor-McCourt (2004)
Investigation of three new mouse mammary tumor cell lines as models for transforming growth factor (TGF)-β and Neu pathway signaling studies: identification of a novel model for TGF-β-induced epithelial-to-mesenchymal transitionBreast Cancer Research, 6
C. Bajdik, B. Kuo, S. Rusaw, Steven Jones, A. Brooks-Wilson (2005)
CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genesBMC Bioinformatics, 6
Hawoong Jeong, S. Mason, A. Barabási, Z. Oltvai (2001)
Lethality and centrality in protein networksNature, 411
Avi Ma’ayan, S. Jenkins, Susana Neves, Anthony Hasseldine, E. Grace, Benjamin Dubin-Thaler, N. Eungdamrong, G. Weng, Prahlad Ram, J. Rice, A. Kershenbaum, G. Stolovitzky, R. Blitzer, R. Iyengar (2005)
Formation of Regulatory Patterns During Signal Propagation in a Mammalian Cellular NetworkScience, 309
P. Rodriguez-Viciana, O. Tetsu, K. Oda, J. Okada, K. Rauen, F. McCormick (2005)
Cancer targets in the Ras pathway.Cold Spring Harbor symposia on quantitative biology, 70
J. Natarajan, D. Berrar, W. Dubitzky, C. Hack, Yonghong Zhang, Catherine DeSesa, J. Brocklyn, E. Bremer (2006)
Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell lineBMC Bioinformatics, 7
Article number: 2006.0019
Kanae Oda, H. Kitano (2006)
A comprehensive map of the toll-like receptor signaling networkMolecular Systems Biology, 2
G. Balázsi, A. Barabási, Z. Oltvai (2005)
Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coliProceedings of the National Academy of Sciences of the United States of America, 102
Qinghua Cui, Zhenbao Yu, E. Purisima, E. Wang (2006)
Principles of microRNA regulation of a human cellular signaling networkMolecular Systems Biology, 2
M. Iorio, M. Ferracin, Chang-gong Liu, A. Veronese, R. Spizzo, S. Sabbioni, E. Magri, M. Pedriali, M. Fabbri, M. Campiglio, S. Ménard, J. Palazzo, A. Rosenberg, P. Musiani, S. Volinia, I. Nenci, G. Calin, P. Querzoli, M. Negrini, C. Croce (2005)
MicroRNA gene expression deregulation in human breast cancer.Cancer research, 65 16
Yann Dublanche, Konstantinos Michalodimitrakis, Nico Kümmerer, Mathilde Foglierini, Luis Serrano (2006)
Noise in transcription negative feedback loops: simulation and experimental analysisMolecular Systems Biology, 2
S. Wuchty, Z. Oltvai, A. Barabási (2003)
Evolutionary conservation of motif constituents in the yeast protein interaction networkNature Genetics, 35
A. Hamosh, A. Scott, J. Amberger, C. Bocchini, David Valle, V. McKusick (2004)
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disordersNucleic Acids Research, 33
M. Babu, N. Luscombe, L. Aravind, M. Gerstein, Sarah Teichmann (2004)
Structure and evolution of transcriptional regulatory networks.Current opinion in structural biology, 14 3
D. Angeli, J. Ferrell, Eduardo Sontag (2004)
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systemsProceedings of the National Academy of Sciences of the United States of America, 101
C. Alberti (2006)
Prostate cancer progression and surrounding microenvironment.The International journal of biological markers, 21 2
Ole Petersen, Helga Nielsen, T. Gudjonsson, R. Villadsen, Lone Rønnov-Jessen, M. Bissell (2001)
The plasticity of human breast carcinoma cells is more than epithelial to mesenchymal conversionBreast Cancer Research : BCR, 3
T. Jenssen, A. Lægreid, J. Komorowski, E. Hovig (2001)
A literature network of human genes for high-throughput analysis of gene expressionNature Genetics, 28
N. Luscombe, M. Babu, Haiyuan Yu, M. Snyder, S. Teichmann, M. Gerstein (2004)
Genomic analysis of regulatory network dynamics reveals large topological changesNature, 431
T. Dewey, D. Galas (2001)
Dynamic models of gene expression and classificationFunctional & Integrative Genomics, 1
Pall Jonsson, T. Cavanna, D. Zicha, P. Bates (2006)
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasisBMC Bioinformatics, 7
M. Bissell, D. Radisky (2001)
Putting tumours in contextNature Reviews Cancer, 1
Hiroaki Kitano, Kanae Oda (2006)
Robustness trade-offs and host–microbial symbiosis in the immune systemMolecular Systems Biology, 2
Xin-yu Zhang, Ying Hu, Yong-Ping Cui, Xiao-ping Miao, Feng Tian, Yongjing Xia, Yiqing Wu, Xiangjun Liu (2006)
Integrated genome‐wide gene expression map and high‐resolution analysis of aberrant chromosomal regions in squamous cell lung cancerFEBS Letters, 580
R. Hoffmann, A. Valencia (2005)
Implementing the iHOP concept for navigation of biomedical literatureBioinformatics, 21 Suppl 2
A. Barabási, Z. Oltvai (2004)
Network biology: understanding the cell's functional organizationNature Reviews Genetics, 5
T. Sørlie, Yulei Wang, Chunlin Xiao, H. Johnsen, B. Naume, R. Samaha, A. Børresen-Dale (2006)
Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platformsBMC Genomics, 7
Lan Zhang, Oliver King, Sharyl Wong, Debra Goldberg, A. Tong, Guillaume Lesage, Brenda Andrews, Howard Bussey, Charles Boone, Frederick Roth (2005)
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction networkJournal of Biology, 4
Hunter Fraser, Aaron Hirsh, L. Steinmetz, C. Scharfe, M. Feldman (2002)
Evolutionary Rate in the Protein Interaction NetworkScience, 296
S. Wuchty (2004)
Evolution and topology in the yeast protein interaction network.Genome research, 14 7
S. Mangan, A. Zaslaver, U. Alon (2003)
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks.Journal of molecular biology, 334 2
T. Billiar, D. Camp, G. Casella, M. Choudhry, Charles Cooper, Constance Elson, Bradley Freeman, R. Gamelli, Celeste Campbell-Finnerty, N. Gibran, D. Hayden, B. Harbrecht, David Herndon, J. Horton, W. Hubbard, J. Hunt, Jeffrey Johnson, M. Klein, J. Lederer, T. Logvinenko, R. Maier, J. Mannick, Philip Mason, B. McKinley, J. Minei, Ernest Moore, F. Moore, A. Nathens, G. O’Keefe, L. Rahme, D. Remick, D. Schoenfeld, M. Schwacha, M. Shapiro, G. Silver, Richard Smith, John Storey, M. Toner, H. Warren (2005)
A network-based analysis of systemic inflammation in humansNature, 437
J. McCallum, S. Ganesh (2003)
Text mining of DNA sequence homology searches.Applied bioinformatics, 2 3 Suppl
V. Ling, A. Chambers, J. Harris, R. Hill (1984)
Dynamic heterogeneity and metastasisJournal of Cellular Physiology, 121
R. Hoffmann, Martin Krallinger, E. Andrés, J. Tamames, C. Blaschke, A. Valencia (2005)
Text Mining for Metabolic Pathways, Signaling Cascades, and Protein NetworksScience's STKE, 2005
E. Eskin, Eugene Agichtein (2003)
Combining Text Mining and Sequence Analysis to Discover Protein Functional RegionsPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
L. Franke, H. Bakel, L. Fokkens, E. Jong, M. Egmont-Petersen, C. Wijmenga (2006)
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.American journal of human genetics, 78 6
S. Wachi, K. Yoneda, R. Wu (2005)
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissuesBioinformatics (Oxford, England), 21
A. Chambers, J. Harris, V. Ling, R. Hill (1984)
Rapid phenotype variation in cells derived from lung metastases of KHT fibrosarcoma.Invasion & metastasis, 4 4
M. Gallegos-Arreola, B. Gómez-Meda, G. Morgan-Villela, M. Arechavaleta-Granell, L. Arnaud-Lopez, T. Beltrán-Jaramillo, R. Gaxiola, G. Zúñiga-González (2004)
GSTT1 Gene Deletion Is Associated with Lung Cancer in Mexican PatientsDisease Markers, 19
J. Harris, A. Chambers, R. Hill, V. Ling (1982)
Metastatic variants are generated spontaneously at a high rate in mouse KHT tumor.Proceedings of the National Academy of Sciences of the United States of America, 79 18
R. Blitzer, J. Connor, George Brown, T. Wong, S. Shenolikar, Ravi Iyengar, E. Landau (1998)
Gating of CaMKII by cAMP-regulated protein phosphatase activity during LTP.Science, 280 5371
T. Taki, M. Taniwaki (2006)
Chromosomal translocations in cancer and their relevance for therapyCurrent Opinion in Oncology, 18
U. Bhalla, Prahlad Ram, R. Iyengar (2002)
MAP Kinase Phosphatase As a Locus of Flexibility in a Mitogen-Activated Protein Kinase Signaling NetworkScience, 297
A. Lièvre, J. Bachet, D. Corre, V. Boige, B. Landi, J. Emile, J. Côté, G. Tomasic, C. Penna, M. Ducreux, P. Rougier, F. Penault-Llorca, P. Laurent-Puig (2006)
KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer.Cancer research, 66 8
S. Hughes, M. Yoshimoto, B. Beheshti, R. Houlston, J. Squire, A. Evans (2006)
The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progressionBMC Genomics, 7
Kanae Oda, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano (2005)
A comprehensive pathway map of epidermal growth factor receptor signalingMolecular Systems Biology, 1
H. Blons, J. Côté, D. Corre, M. Riquet, Elisabeth Fabre-Guilevin, P. Laurent-Puig, C. Danel (2006)
Epidermal Growth Factor Receptor Mutation in Lung Cancer are Linked to Bronchioloalveolar DifferentiationThe American Journal of Surgical Pathology, 30
N. Batada, L. Hurst, M. Tyers (2006)
Evolutionary and Physiological Importance of Hub ProteinsPLoS Computational Biology, 2
Ramazan Saeed, Charlotte Deane (2006)
Protein protein interactions, evolutionary rate, abundance and ageBMC Bioinformatics, 7
Article number: 2005.0006
A. César, Aldenis Borim, Alaor Caetano, P. Cury, A. Silva (2004)
Aneuploidies, deletion, and overexpression of TP53 gene in intestinal metaplasia of patients without gastric cancer.Cancer genetics and cytogenetics, 153 2
S. Mangan, U. Alon (2003)
Structure and function of the feed-forward loop network motifProceedings of the National Academy of Sciences of the United States of America, 100
S. Volinia, G. Calin, Chang-gong Liu, S. Ambs, A. Cimmino, F. Petrocca, R. Visone, M. Iorio, C. Roldo, M. Ferracin, R. Prueitt, N. Yanaihara, G. Lanza, A. Scarpa, A. Vecchione, M. Negrini, C. Harris, C. Croce (2006)
A microRNA expression signature of human solid tumors defines cancer gene targetsProceedings of the National Academy of Sciences of the United States of America, 103
M. Driel, J. Bruggeman, G. Vriend, H. Brunner, J. Leunissen (2006)
A text-mining analysis of the human phenomeEuropean Journal of Human Genetics, 14
P. Futreal, L. Coin, M. Marshall, T. Down, T. Hubbard, R. Wooster, N. Rahman, Michael Stratton (2004)
A census of human cancer genesNature Reviews Cancer, 4
G. Calin, C. Croce (2006)
MicroRNA-cancer connection: the beginning of a new tale.Cancer research, 66 15
F. Bertucci, P. Finetti, J. Rougemont, E. Charafe-Jauffret, N. Cervera, C. Tarpin, C. Nguyen, L. Xerri, R. Houlgatte, J. Jacquemier, P. Viens, D. Birnbaum (2005)
Gene expression profiling identifies molecular subtypes of inflammatory breast cancer.Cancer research, 65 6
E. Wang, E. Purisima (2005)
Network motifs are enriched with transcription factors whose transcripts have short half-lives.Trends in genetics : TIG, 21 9
Cathy Wu, R. Apweiler, A. Bairoch, D. Natale, W. Barker, B. Boeckmann, Serenella Ferro, E. Gasteiger, Hongzhan Huang, R. Lopez, M. Magrane, M. Martin, R. Mazumder, C. O’Donovan, Nicole Redaschi, Baris Suzek (2005)
The Universal Protein Resource (UniProt): an expanding universe of protein informationNucleic Acids Research, 34
L. Sweetlove, A. Fernie (2005)
Regulation of metabolic networks: understanding metabolic complexity in the systems biology era.The New phytologist, 168 1
E. Camon, M. Magrane, D. Barrell, David Binns, W. Fleischmann, P. Kersey, N. Mulder, T. Oinn, J. Maslen, Anthony Cox, R. Apweiler (2003)
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.Genome research, 13 4
K. Brown, I. Jurisica (2005)
Online Predicted Human Interaction DatabaseBioinformatics, 21 9
E. Camon, M. Magrane, D. Barrell, V. Lee, E. Dimmer, J. Maslen, David Binns, Nicola Harte, R. Lopez, R. Apweiler (2004)
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene OntologyNucleic acids research, 32 Database issue
Genomic alterations lead to cancer complexity and form a major hurdle for comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe recent advances in studying cancer-associated genes from a systems biology point of view. The integration of known cancer genes onto protein and signaling networks reveals the characteristics of cancer genes within networks. This approach shows that cancer genes often function as network hub proteins which are involved in many cellular processes and form focal nodes in information exchange between many signaling pathways. Literature mining allows constructing gene-gene networks, in which new cancer genes can be identified. The gene expression profiles of cancer cells are used for reconstructing gene regulatory networks. By doing so, genes which are involved in the regulation of cancer progression can be picked up from these networks, after which their functions can be further confirmed in the laboratory.
Cellular and Molecular Life Sciences – Springer Journals
Published: Apr 6, 2007
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