Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm

Journal of Molecular Biology

Volumn 318, Issue 1, 2002, Pages 71-81

  Zhu, Zhou ^a   Pilpel, Yitzhak ^a   Church, George M ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Clustering; Computational biology; DNA regulatory motif; Expression profile; Transcription factor

Indexed keywords

TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BINDING SITE; CELL CYCLE; CLUSTER ANALYSIS; COMPUTER MODEL; CONTROLLED STUDY; FACILITATION; GENE CONTROL; HYPOTHESIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE; SAMPLING; SPOROGENESIS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036300823     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00026-8     Document Type: Article

References (27)

1. Analysis and modeling of DNA-protein interactions
2. Cluster analysis and display of genome-wide expression patterns
3. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
4. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
5. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
6. Systematic determination of genetic network architecture
7. Predicting gene regulatory elements in silico on a genomic scale
8. Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae
9. Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80
10. Exploring the metabolic and genetic control of gene expression on a genomic scale
11. cis Element/transcription factor analysis (cis/TF): A method for discovering transcription factor/cis element relationships
12. The transcriptional program of sporulation in budding yeast
13. Serial regulation of transcriptional regulators in the yeast cell cycle
14. Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism
15. Glucose repression in yeast
16. RAP1: A protean regulator in yeast
17. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
18. A genome-wide transcriptional analysis of the mitotic cell cycle
19. Regulatory element detection using correlation with expression
20. Functional discovery via a compendium of expression profiles
21. Systematic management and analysis of yeast gene expression data
22. MIPS: A database for genomes and protein sequences
23. Multiple interactions control the expression of yeast genes
24. SCPD: A promoter database of the yeast Saccharomyces cerevisiae
25. Predicting regulons and their cis-regulatory motifs by comparative genomics
26. Identifying regulatory networks by combinatorial analysis of promoter elements
27. Sequence logos: A new way to display consensus sequences