Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae.
BACKGROUND
We demonstrate a computational process by which transcription factor binding sites can be elucidated using genome-wide expression and binding profiles. The profiles direct us to the intergenic locations likely to contain the promoter regions for a given factor. These sequences are multiply and locally aligned to give an anchor motif from which further characterization can take place.


RESULTS
We present bases for and assumptions about the variability within these motifs which give rise to potentially more accurate motifs, capture complex binding sites built upon the basis motif, and eliminate the constraints of the currently employed promoter searching protocols. We also present a measure of motif quality based on the occurrence of the putative motifs in regions observed to contain the binding sites. The assumptions, motif generation, quality assessment and comparison allow the user as much control as their a priori knowledge allows.


BACKGROUND
IGRDB and the datasets mentioned herein are available at http://chipdb.wi.mit.edu/
Harrison
Rhonda
R
Bioinformatics Department, Boston University, 44 Cummington Street, Boston, MA 02215, USA. rhonda@bu.edu
DeLisi
Charles
C
D020816:Amino Acid Motifs; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D016384:Consensus Sequence / Q000235:genetics; D004268:DNA-Binding Proteins; D003628:Database Management Systems; D030541:Databases, Genetic; D030562:Databases, Protein; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D011485:Protein Binding / Q000235:genetics; D011786:Quality Control; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*
D004268:DNA-Binding Proteins; D005656:Fungal Proteins; C052130:GAL4 protein, S cerevisiae; C489241:STE12 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors