PathExpress update: The enzyme neighbourhood method of associating gene-expression data with metabolic pathways

Nucleic Acids Research

Volumn 37, Issue SUPPL. 2, 2009, Pages

  Goffard, Nicolas ^a,b   Frickey, Tancred ^a   Weiller, Georg ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b INSTITUT LOUIS MALARDÉ   (French Polynesia)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BARREL MEDIC; COMPUTER PROGRAM; DATA BASE; ENZYME METABOLISM; ENZYME NEIGHBOURHOOD; GENE EXPRESSION; GENOMICS; INTERNET; NONHUMAN; PLANT ROOT; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEOMICS;

ENZYMES; GENE EXPRESSION PROFILING; INTERNET; MEDICAGO TRUNCATULA; METABOLIC NETWORKS AND PATHWAYS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 67849116896     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp432     Document Type: Article

References (36)

1. Breitling,R. (2006) Biological microarray interpretation: The rules of engagement. Biochim. Biophys. Acta, 1759, 319-327.
2. Cui,X. and Churchill,G.A. (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol., 4, 210.
3. Ashburner,M., Ball,C., Blake,J., Botstein,D., Butler,H., Cherry,J., Davis,A., Dolinski,K., Dwight,S., Eppig,J. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
4. Huang,D.W., Sherman,B.T. and Lempicki,R.A. (2009) Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
5. Kanehisa,M. and Goto,S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
6. Okuda,S., Yamada,T., Hamajima,M., Itoh,M., Katayama,T., Bork,P., Goto,S. and Kanehisa,M. (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res., 36, W423-W426.
7. Caspi,R., Foerster,H., Fulcher,C.A., Hopkinson,R., Ingraham,J., Kaipa,P., Krummenacker,M., Paley,S., Pick,J., Rhee,S.Y. et al. (2006) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res., 34, D511-D516.
8. Baitaluk,M., Sedova,M., Ray,A. and Gupta,A. (2006) BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res., 34, W466-W471.
9. Chung,H.J., Park,C.H., Han,M.R., Lee,S., Ohn,J.H., Kim,J., Kim,J. and Kim,J.H. (2005) ArrayXPath II: Mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res., 33, W621-W626.
10. Goffard,N. and Weiller,G. (2007) PathExpress: A web-based tool to identify relevant pathways in gene expression data. Nucleic Acids Res., 35, W176-W181.
11. Mlecnik,B., Scheideler,M., Hackl,H., Hartler,J., Sanchez-Cabo,F. and Trajanoski,Z. (2005) PathwayExplorer: Web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res., 33, W633-W637.
12. Pan,D., Sun,N., Cheung,K.H., Guan,Z., Ma,L., Holford,M., Deng,X. and Zhao,H. (2003) PathMAPA: A tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics, 4, 56.
13. Pandey,R., Guru,R. and Mount,D. (2004) Pathway miner: Extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics, 20, 2156-2158.
14. Salomonis,N., Hanspers,K., Zambon,A.C., Vranizan,K., Lawlor,S.C., Dahlquist,K.D., Doniger,S.W., Stuart,J., Conklin,B.R. and Pico,A.R. (2007) GenMAPP 2: New features and resources for pathway analysis. BMC Bioinformatics, 8, 217.
15. Thimm,O., Bläsing,O., Gibon,Y., Nagel,A., Meyer,S., Krüger,P., Selbig,J., Müller,L.A., Rhee,S.Y. and Stitt,M. (2004) MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37 914-939.
16. Wu,J., Mao,X., Cai,T., Luo,J. and Wei,L. (2006) KOBAS server: A web-based platform for automated annotation and pathway identification. Nucleic Acids Res., 34, W720-W724.
17. Ideker,T., Ozier,O., Schwikowski,B. and Siegel,A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240.
18. Cline,M.S., Smoot,M., Cerami,E., Kuchinsky,A., Landys,N., Workman,C., Christmas,R., Avila-Campilo,I., Creech,M., Gross,B. et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc., 2, 2366-2382.
19. Hanisch,D., Zien,A., Zimmer,R. and Lengauer,T. (2002) Co-clustering of biological networks and gene expression data. Bioinformatics, 18(Suppl. 1), S145-S154.
20. König,R. and Eils,R. (2004) Gene expression analysis on biochemical networks using the Potts spin model. Bioinformatics, 20, 1500-1505.
21. Rapaport,F., Zinovyev,A., Dutreix,M., Barillot,E. and Vert,J.P. (2007) Classification of microarray data using gene networks. BMC Bioinformatics, 8, 35.
22. Schuster,S., Pfeiffer,T., Moldenhauer,F., Koch,I. and Dandekar,T. (2002) Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18, 351-361.
23. Schwartz,J.M., Gaugain,C., Nacher,J.C., de Daruvar,A. and Kanehisa,M. (2007) Observing metabolic functions at the genome scale. Genome Biol., 8, R123.
24. Goto,S., Nishioka,T. and Kanehisa,M. (1998) LIGAND: Chemical database for enzyme reactions. Bioinformatics, 14, 591-599.
25. Goto,S., Okuno,Y., Hattori,M., Nishioka,T. and Kanehisa,M. (2002) LIGAND: Database of chemical compounds and reactions in biological pathways. Nucleic Acids Res., 30, 402-404.
26. Holmes,P., Goffard,N., Weiller,G.F., Rolfe,B.G. and Imin,N. (2008) Transcriptional profiling of Medicago truncatula meristematic root cells. BMC Plant Biol., 8, 21.
27. Sackmann,A., Heiner,M. and Koch,I. (2006) Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics, 7, 482.
28. Green,M.L. and Karp,P.D. (2005) Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res., 33, 4035-4039.
29. Liu,G., Loraine,A.E., Shigeta,R., Cline,M., Cheng,J., Valmeekam,V., Sun,S., Kulp,D. and Siani-Rose,M.A. (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res., 31, 82-86.
30. The UniProt Consortium. (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190-D195.
31. Cho,R.J., Huang,M., Campbell,M.J., Dong,H., Steinmetz,L., Sapinoso,L., Hampton,G., Elledge,S.J., Davis,R.W. and Lockhart,D.J. (2001) Transcriptional regulation and function during the human cell cycle. Nat. Genet., 27, 48-54.
32. Bonferroni,C. (1936) Teoria statistica delle classi e calcolo delle probabilità. Pubblicazioni del Regio Istituto Superiore di Scienze Economiche e Commerciali di Firenze, 8, 3-62.
33. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Statist. Soc. B., 57, 289-300.
34. Edgar,R., Domrachev,M. and Lash,A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
35. Antonov,A.V., Dietmann,S. and Mewes,H.W. (2008) KEGG spider: interpretation of genomics data in the context of the global gene metabolic network. Genome Biol., 9, R179.
36. Dam,S., Laursen,B.S., Ornfelt,J.H., Jochimsen,B., Staerfeldt,H.H., Friis,C., Nielsen,K., Goffard,N., Besenbacher,S., Krusell,L. et al. (2009) The proteome of seed development in the model legume Lotus japonicus. Plant Physiol., 149, 1325-1340.