A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes

Journal of Computational Biology

Volumn 9, Issue 2, 2002, Pages 447-464

  Thijs, Gert ^a   Marchal, Kathleen ^a   Lescot, Magali ^a   Rombauts, Stephane ^a   De Moor, Bart ^a   Rouzé, Pierre ^a   Moreau, Yves ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Cribbs sampling; Gene expression; Microarray; Motif finding; Regulatory elements

Indexed keywords

METHIONINE;

ALGORITHM; ARABIDOPSIS; CONFERENCE PAPER; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

ALGORITHMS; ARABIDOPSIS; BACTERIA; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA; GENE EXPRESSION PROFILING; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036108622     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/10665270252935566     Document Type: Conference Paper

References (44)

1. Whole-genome expression analysis: Challenges beyond clustering
2. Detection of eukaryotic promoters using Markov transition matrices
3. Unsupervised learning of multiple motifs in biopolymers using expectation maximization
4. Wound signaling in tomato plants. Evidence that aba is not a primary signal for defense gene activation
5. Regulatory elements and expression profiles
6. Adaptive quality-based clustering of gene expression profiles
7. Improved microbial gene identification with glimmer
8. Cluster analysis and display of genome-wide expression patterns
9. Exploring expression data: Identification and analysis of coexpressed genes
10. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
11. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
12. Two methods for improving performance of an HMM and their application for gene finding
13. Detecting subbtle sequence signals: A Gibbs sampling strategy for multiple alignment
14. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
15. Bayesian models for multiple local sequence alignment and gibbs sampling strategies
16. Bioprospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
17. Genomics, gene expression and DNA arrays
18. GeneMark.hmm: New solutions for gene finding
19. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
20. From coexpression to coregulation: An approach to inferring transcriptional regulation among gene classes from large-scale expression data
21. Interpolated Markov chains for eukaryotic promotor recognition
22. Identification and analysis of eukaryotic promoters: Recent computational approaches
23. Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
24. Abscisic acid is involved in the wound-induced expression of the proteinase inhibitor II gene potato and tomato
25. Jasmonate and salicylate as global signals for defense gene expression
26. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis
27. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole genome mRNA quantitation
28. Identification of a methyl jasmonate-responsive region in the promoter of a lipoxygenase-1 gene expressed in barley grain
29. Analysis of large-scale gene expression data
30. A statistical method for finding transcription factor binding sites
31. Genetic network analysis in light of massively parallel biological data acquisition
32. Systematic determination of genetic network architecture
33. A higher order background model improves the detection of promoter regulatory elements by Gibbs sampling
34. INCLUSive: INtegrated CLustering, Upstream sequence retrieval and motif Sampling
35. An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
36. Extracting regulatory sites from upstream region of yeast genes by computational analysis of oligonucleotide frequencies
37. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
38. A web site for the computational analysis of yeast regulatory sequences
39. 80 family of promoter signals
40. Large-scale temporal gene expression mapping of central nervous system development
41. ANN-SPEC: A method for discovering transcription binding sites with improved specificity
42. Large-scale gene expression data analysis: A new challenge to computational biologists
43. Cluster, function and promoter: Analysis of yeast expression array