Classification of microarray data using gene networks

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Rapaport, Franck ^a,b   Zinovyev, Andrei ^a   Dutreix, Marie ^c   Barillot, Emmanuel ^a   Vert, Jean Philippe ^b  

^a INSTITUT CURIE   (France)

^b PSL RESEARCH UNIVERSITY   (France)

^c CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INTERPRETATION; BIOLOGICAL SIGNIFICANCE; CLASSIFICATION PERFORMANCE; GENE EXPRESSION DATA; GENE EXPRESSION PROFILES; HIGH FREQUENCY COMPONENTS; SPECTRAL DECOMPOSITION; SUPERVISED CLASSIFICATION;

EIGENVALUES AND EIGENFUNCTIONS; GENE EXPRESSION; MICROARRAYS; TOPOLOGY;

CLASSIFICATION (OF INFORMATION);

ASPARAGINE; CHLOROPHYLL; CITRIC ACID; DNA POLYMERASE; ERGOSTEROL; FOLIC ACID; GLYCAN; LYSINE; NITROGEN; PHENYLALANINE; PORPHYRIN; PROTEIN KINASE; PYRIMIDINE; RIBOFLAVIN; RNA POLYMERASE; STEROL; SULFUR; TRYPTOPHAN; TYROSINE; PROTEOME;

ALGORITHM; AMINO ACID METABOLISM; AMINO ACID SYNTHESIS; ARTICLE; ATTENUATION; CITRIC ACID CYCLE; CLASSIFICATION; CONTROLLED STUDY; DATA ANALYSIS; FREQUENCY ANALYSIS; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC ANALYSIS; GLUCONEOGENESIS; GLYCOLYSIS; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; NITROGEN METABOLISM; NONHUMAN; OXIDATIVE PHOSPHORYLATION; PORPHYRIN METABOLISM; PRINCIPAL COMPONENT ANALYSIS; PYRIMIDINE METABOLISM; STATISTICAL ANALYSIS; STEROL METABOLISM; STRAIN DIFFERENCE; SUPPORT VECTOR MACHINE; VITAMIN METABOLISM; YEAST; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; DNA MICROARRAY; EVALUATION STUDY; GENE EXPRESSION; METABOLISM; PHYSIOLOGY; PROCEDURES; SIGNAL TRANSDUCTION;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PROTEOME; SIGNAL TRANSDUCTION;

EID: 33847162049     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-35     Document Type: Article

References (36)

1. Consortium TGO Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000 25 25-29 10802651
2. http://www.biocarta.com
3. http://www.genmapp.com
4. Kanehisa M Goto S Kawashima S Okuno Y Hattori M The KEGG resource for deciphering the genome Nucleic Acids Res 2004 32 Database D277-80 308797 14681412
5. Hosack D Dennis G Sherman B Lane H Lempicki R Identifying biological themes within lists of genes with EASE Genome Biology 2003 R70 1-7
6. Breslin T Krogh M Peterson C Troein C Signal transduction pathway profiling of individual tumor samples BMC Bioinformatics 2005 6 163 1184060 15987529
7. Thomas R Kaufman M Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits Chaos 2001 11 180-195 12779452
8. Radulescu O Lagarrigue S Siegel A Le Borgne M Veber P Topology and static response of interaction networks in molecular biology J R Soc Interface 2005
9. Gat-Viks I Tanay A Shamir R Modeling and analysis of heterogeneous regulation in biological networks J Comput Biol 2004 11 6 1034-49 15662196
10. Curtis KR Oresic M Vidal-Puig A Pathways to the analysis of microarray data Trends in Biotechnology 2005 23 8 429-435 15950303
11. Cavalieri D De Filippo C Bioinformatic methods for integrating whole-genome expression results into cellular networks Drug Discov Today 2005 10 10 727-34 15896686
12. Krull M Pistor S Voss N Kel A Reuter I Kronenberg D Michael H Schwarzer K Potapov A Choi C Kel-Margoulis O Wingender E TRANSPATH: An information resource for storing and visualizing signaling pathways and their pathological aberrations Nucleic Acids Res 2006 34 Database D546-51 1347469 16381929
13. Karp PD Ouzounis CA Moore-Kochlacs C Goldovsky L Kaipa P Ahren D Tsoka S Darzentas N Kunin V Lopez-Bigas N Expansion of the BioCyc collection of pathway/genome databases to 160 genomes Nucleic Acids Res 2005 33 19 6083-9 1266070 16246909
14. Joshi-Tope G Gillespie M Vastrik I D'Eustachio P Schmidt E de Bono B Jassal B Gopinath GR Wu GR Matthews L Lewis S Birney E Stein L Reactome: a knowledgebase of biological pathways Nucleic Acids Res 2005 33 Database D428-32 [1362-4962 (Electronic) Journal Article]. 540026 15608231
15. Vert JP Kanehisa M Extracting active pathways from gene expression data Bioinformatics 2003 19 Suppl 2 II238-II244 14534196
16. Rahnenfuhrer J Domingues F Maydt J Lengauer T Calculating the statistical significance of changes in pathway activity from gene expression data Statistical Applications in Genetics and Molecular Biology 2004 3 Article 16
17. Hanisch D Zien A Zimmer R Lengauer T Co-clustering of biological networks and gene expression data Bioinformatics 2002 12169542
18. Liao JC Boscolo R Yang YL Tran LM Sabatti C Roychowdhury VP Network component analysis: Reconstruction of regulatory signals in biological systems Proc Natl Acad Sci USA 2003 100 26 15522-7 307600 14673099
19. Galbraith SJ Tran LM Liao JC Transcriptome network component analysis with limited microarray data Bioinformatics 2006 22 15 1886-94 16766556
20. Babur O Demir E Ayaz A Dogrusoz U Sakarya O Pathway activity inference using microarray data Technical report, Bilkent Center for Bioinformatics (BCBI) 2004
21. Sivachenko A Yuriev A Daraselia N Mazo I Identifying Local Gene Expression Patterns in Biomolecular Networks Proceedings of 2005 IEEE Computational Systems Bioinformatics Conference, Stanford, California 2005
22. Kelley R Ideker T Systematic interpretation of genetic interactions using protein networks Nat Biotechnol 2005 23 5 561-566 15877074
23. van Helden J Gilbert D Wernisch L Schroeder M Wodak SJ Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data JOBIM '00: Selected papers from the First International Conference on Computational Biology, Biology, Informatics, and Mathematics London, UK: Springer-Verlag 2001 147-164
24. Kharchenko P Vitkup D Church GM Filling gaps in a metabolic network using expression information Bioinformatics 2004 20 Suppl 1 I178-I185 15262797
25. Kharchenko P Chen L Freund Y Vitkup D Church GM Identifying metabolic enzymes with multiple types of association evidence BMC Bioinformatics 2006 7 177 1450304 16571130
26. Mercier G Berthault N Mary J Peyre J Antoniadis A Comet JP Cornuejols A Froidevaux C Dutreix M Biological detection of low radiation doses by combining results of two microarray analysis methods Nucleic Acids Res 2004 32 e12 373305 14722227
27. Jolliffe I Principal component analysis New-York: Springer-Verlag 1996
28. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003 13 11 2498-504 403769 14597658
29. Mercier G Denis Y Marc P Picard L Dutreix M Transcriptional induction of repair genes during slowing of replication in irradiated Saccharomyces cerevisiae Mutat Res 2001 487 3-4 157-172 11738942
30. Stuart JM Segal E Koller D Kim SK A gene-coexpression network for global discovery of conserved genetic modules Science 2003 302 5643 249-55 12934013
31. Chung FRK Spectral graph theory, Volume 92 of CBMS Regional Conference Series Providence: American Mathematical Society 1997
32. Mohar B Some applications of Laplace eigenvalues of graphs Graph Symmetry: Algebraic Methods and Applications, Volume 497 of NATO ASI Series C Dordrecht: Kluwer Hahn G, Sabidussi G 1997 227-275
33. Schölkopf B Smola AJ Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond Cambridge, MA: MIT Press 2002
34. Schölkopf B Tsuda K Vert JP Kernel Methods in Computational Biology MIT Press 2004
35. Boser BE Guyon IM Vapnik VN A training algorithm for optimal margin classifiers Proceedings of the 5th annual ACM workshop on Computational Learning Theory ACM Press 1992 144-152
36. Hastie T Tibshirani R Friedman J The elements of statistical learning: data mining, inference, and prediction. Springer 2001