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Genome Res
2001 Jan 01;111:112-23. doi: 10.1101/gr.148301.
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Assessing clusters and motifs from gene expression data.
Jakt LM
,
Cao L
,
Cheah KS
,
Smith DK
.
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Large-scale gene expression studies and genomic sequencing projects are providing vast amounts of information that can be used to identify or predict cellular regulatory processes. Genes can be clustered on the basis of the similarity of their expression profiles or function and these clusters are likely to contain genes that are regulated by the same transcription factors. Searches for cis-regulatory elements can then be undertaken in the noncoding regions of the clustered genes. However, it is necessary to assess the efficiency of both the gene clustering and the postulated regulatory motifs, as there are many difficulties associated with clustering and determining the functional relevance of matches to sequence motifs. We have developed a method to assess the potential functional significance of clusters and motifs based on the probability of finding a certain number of matches to a motif in all of the gene clusters. To avoid problems with threshold scores for a match, the top matches to a motif are taken in several sample sizes. Genes from a sample are then counted by the cluster in which they appear. The probability of observing these counts by chance is calculated using the hypergeometric distribution. Because of the multiple sample sizes, strong and weak matching motifs can be detected and refined and significant matches to motifs across cluster boundaries are observed as all clusters are considered. By applying this method to many motifs and to a cluster set of yeast genes, we detected a similarity between Swi Five Factor and forkhead proteins and suggest that the currently unidentified Swi Five Factor is one of the yeast forkhead proteins.
Althoefer,
Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae.
1995, Pubmed
Althoefer,
Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae.
1995,
Pubmed
Ben-Dor,
Clustering gene expression patterns.
1999,
Pubmed
Bittner,
Data analysis and integration: of steps and arrows.
1999,
Pubmed
Bowtell,
Options available--from start to finish--for obtaining expression data by microarray.
1999,
Pubmed
Brown,
Knowledge-based analysis of microarray gene expression data by using support vector machines.
2000,
Pubmed
Bucher,
Regulatory elements and expression profiles.
1999,
Pubmed
Carulli,
High throughput analysis of differential gene expression.
1998,
Pubmed
Cho,
A genome-wide transcriptional analysis of the mitotic cell cycle.
1998,
Pubmed
Chu,
The transcriptional program of sporulation in budding yeast.
1998,
Pubmed
Corpet,
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.
2000,
Pubmed
Costanzo,
The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information.
2000,
Pubmed
DeRisi,
Exploring the metabolic and genetic control of gene expression on a genomic scale.
1997,
Pubmed
Eisen,
Cluster analysis and display of genome-wide expression patterns.
1998,
Pubmed
Fickett,
Eukaryotic promoter recognition.
1997,
Pubmed
Frech,
Software for the analysis of DNA sequence elements of transcription.
1997,
Pubmed
Gaasterland,
Making the most of microarray data.
2000,
Pubmed
Gajiwala,
Winged helix proteins.
2000,
Pubmed
Hermann-Le Denmat,
Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a fork head protein involved in rRNA processing.
1994,
Pubmed
Hertz,
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
1999,
Pubmed
Hertz,
Identification of consensus patterns in unaligned DNA sequences known to be functionally related.
1990,
Pubmed
Heyer,
Exploring expression data: identification and analysis of coexpressed genes.
1999,
Pubmed
Hofmann,
The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors.
1995,
Pubmed
Hughes,
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.
2000,
Pubmed
Häcker,
The Drosophila fork head domain protein crocodile is required for the establishment of head structures.
1995,
Pubmed
Kaufmann,
DNA recognition site analysis of Xenopus winged helix proteins.
1995,
Pubmed
,
Xenbase
Koranda,
Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters.
2000,
Pubmed
Kumar,
Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase.
,
Pubmed
Lascaris,
DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences.
1999,
Pubmed
Lydall,
A new role for MCM1 in yeast: cell cycle regulation of SW15 transcription.
1991,
Pubmed
McInerny,
A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription.
1997,
Pubmed
McIntosh,
MCB elements and the regulation of DNA replication genes in yeast.
1993,
Pubmed
Mewes,
Overview of the yeast genome.
1997,
Pubmed
Overdier,
The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix.
1994,
Pubmed
Overdier,
The winged helix transcriptional activator HFH-3 is expressed in the distal tubules of embryonic and adult mouse kidney.
1997,
Pubmed
Pedersen,
The biology of eukaryotic promoter prediction--a review.
1999,
Pubmed
Peterson,
The winged helix transcriptional activator HFH-8 is expressed in the mesoderm of the primitive streak stage of mouse embryos and its cellular derivatives.
1997,
Pubmed
Pic,
The forkhead protein Fkh2 is a component of the yeast cell cycle transcription factor SFF.
2000,
Pubmed
Pierrou,
Cloning and characterization of seven human forkhead proteins: binding site specificity and DNA bending.
1994,
Pubmed
Quandt,
MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.
1995,
Pubmed
Roth,
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.
1998,
Pubmed
Schneider,
Sequence logos: a new way to display consensus sequences.
1990,
Pubmed
Smith,
A major component approach to presenting consensus sequences.
1998,
Pubmed
Spellman,
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
1998,
Pubmed
Tamayo,
Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation.
1999,
Pubmed
Tavazoie,
Systematic determination of genetic network architecture.
1999,
Pubmed
Taylor,
Characterization of the DNA-binding domains from the yeast cell-cycle transcription factors Mbp1 and Swi4.
2000,
Pubmed
Thompson,
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
1994,
Pubmed
Velculescu,
Characterization of the yeast transcriptome.
1997,
Pubmed
Wen,
Large-scale temporal gene expression mapping of central nervous system development.
1998,
Pubmed
Wingender,
TRANSFAC: an integrated system for gene expression regulation.
2000,
Pubmed
Yada,
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
1998,
Pubmed
Zhu,
The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes the calmodulin-binding protein in the yeast spindle pole body.
1998,
Pubmed
Zhu,
SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
1999,
Pubmed
Zhu,
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth.
2000,
Pubmed
