DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Blom, Evert Jan ^a   van Hijum, Sacha A F T ^a,b,c   Hofstede, Klaas J ^a   Silvis, Remko ^a   Roerdink, Jos B T M ^d   Kuipers, Oscar P ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF GREIFSWALD   (Germany)

^c NIZO FOOD RESEARCH   (Netherlands)

^d UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EXPRESSION PATTERNS; FUNCTIONAL ANNOTATION; GENE EXPRESSION DATA; PERFORMANCE MEASURE; PUTATIVE TRANSCRIPTION FACTORS; RESEARCH COMMUNITIES; TIME-COURSE EXPERIMENTS; TRANSCRIPTIONAL CONTROL;

APPLICATION PROGRAMS; CLUSTER ANALYSIS; CLUSTERING ALGORITHMS; GENE EXPRESSION; RESEARCH;

BENCHMARKING;

TRANSCRIPTION FACTOR; TRANSCRIPTOME; DNA;

ARTICLE; BINDING SITE; CLUSTER ANALYSIS; COMPUTER PROGRAM; DNA SEQUENCE; DNA STRUCTURE; GENE CLUSTER; GENETIC ALGORITHM; TRANSCRIPTION REGULATION; ALGORITHM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY;

PROKARYOTA;

ALGORITHMS; BINDING SITES; CLUSTER ANALYSIS; DNA; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 63449087899     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-535     Document Type: Article

References (24)

1. Quackenbush J Computational analysis of microarray data Nat Rev Genet 2001, 2(6):418-427. 10.1038/35076576 11389458
2. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
3. Toronen P Selection of informative clusters from hierarchical cluster tree with gene classes BMC Bioinformatics 2004, 5:32. 407846 15043761 10.1186/1471-2105-5-32
4. Gat-Viks I Sharan R Shamir R Scoring clustering solutions by their biological relevance Bioinformatics 2003, 9(18):2381-2389. 10.1093/ bioinformatics/btg330
5. Gibbons FD Roth FP Judging the quality of gene expression-based clustering methods using gene annotation Genome Res 2002, 12(10):1574-1581. 187526 12368250 10.1101/gr.397002
6. Gasch AP Eisen MB Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering Genome Biol 2002, 3:11. RESEARCH0059 133443 12429058 10.1186/gb-2002-3-11-research0059
7. Shamir R Maron-Katz A Tanay A Linhart C Steinfeld I Sharan R Shiloh Y Elkon R EXPANDER-an integrative program suite for microarray data analysis BMC Bioinformatics 2005, 6:232. 1261157 16176576 10.1186/ 1471-2105-6-232
8. Kim TM Chung YJ Rhyu MG Jung MH Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis BMC Bioinformatics 2007, 8:453. 2217565 18021416 10.1186/1471-2105-8-453
9. Datta S Datta S Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes BMC Bioinformatics 2006, 7:397. 1590054 16945146 10.1186/1471-2105-7-397
10. Jakt LM Cao L Cheah KS Smith DK Assessing clusters and motifs from gene expression data Genome Res 2001, 11:112-123. 311053 11156620 10.1101/ gr.148301
11. Thijs G Moreau Y Smet FD Mathys J Lescot M Rombauts S Rouze P Moor BD Marchal K INCLUSive: Integrated clustering, upstream sequence retrieval and motif sampling Bioinformatics 2002, 18(2):331-332. 10.1093/ bioinformatics/18.2.331 11847086
12. Chakravarty A Carlson J Khetani R Gross R A novel ensemble learning method for de novo computational identification of DNA binding sites BMC Bioinformatics 2007, 8:249. 1950314 17626633 10.1186/1471-2105-8-249
13. Blom EJ Bosman DWJ van Hijum SAFT Breitling R Tijsma L Silvis R Roerdink JBTM Kuipers OP FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes Bioinformatics 2007, 23(9):1161-1163. 10.1093/bioinformatics/btl658 17237043
14. Makita Y Nakao M Ogasawara N Nakai K DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics Nucleic Acids Res 2004, 32(Database):D75-D77. 308808 14681362 10.1093/nar/gkh074
15. Salgado H Gama-Castro S Peralta-Gil M Díaz-Peredo E Sánchez-Solano F Santos-Zavaleta A Martínez-Flores I Jiménez-Jacinto V Bonavides-Martínez C Segura-Salazar J Martínez-Antonio A Collado-Vides J RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Nucleic Acids Res 2006, 34(Database):D394-D397. 1347518 16381895 10.1093/nar/gkj156
16. Crooks GE Hon G Chandonia JM Brenner SE WebLogo: A sequence logo generator Genome Res 2004, 14(6):1188-1190. 419797 15173120 10.1101/ gr.849004
17. Keijser BJF Beek AT Rauwerda H Schuren F Montijn R Spek van der H Brul S Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth J Bacteriol 2007, 189(9):3624-3634. 1855883 17322312 10.1128/JB.01736-06
18. NCBI GEO http://www.ncbi.nlm.nih.gov/geo/
19. Scheer M Klawonn F Münch R Grote A Hiller K Choi C Koch I Schobert M Härtig E Klages U Jahn D JProGO: A novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information Nucleic Acids Res 2006, 34(Web Server):W510-W515. 1538798 16845060 10.1093/nar/gkl329
20. EBI Genome Reviews http://www.ebi.ac.uk/GenomeReviews/files/cellular/
21. COG WHOG ftp://ftp.ncbi.nih.gov/pub/COG/COG/whog
22. KEGG Pathways ftp://ftp.expasy.org/databases/uniprot/current_release/ knowledgebase/taxonomic_divisions/uniprot_sprot_bacteria.dat.gz
23. Gene Ontology Obo File http://www.geneontology.org/ontology/ gene_ontology.obo
24. Uniprot http://www.genome.jp/kegg/catalog/org_list.html