2007
DOI: 10.1093/nar/gkm828
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Abstract: Accurate and comprehensive information about the nucleotide sequence specificity of trans-acting factors (TFs) is essential for computational and experimental analyses of gene regulatory networks. We present the Yeast Transfactome Database, a repository of sequence specificity models and condition-specific regulatory activities for a large number of DNA- and RNA-binding proteins in Saccharomyces cerevisiae. The sequence specificities in TransfactomeDB, represented as position-specific affinity matrices (PSAMs)… Show more

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Cited by 24 publications
(31 citation statements)
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“…We also tried using different PWM models for Gcr1, which came from different experiments. None of these PWMs for Gcr1 are in good agreement with each other, nor do they agree well with our predictions (Harbison et al 2004;MacIsaac et al 2006;Pachkov et al 2007;Foat et al 2008;Spivak and Stormo 2012). The relationship between occupancy at the Gcr1 sites and the sites' effect on gene expression may be complicated by condition-specific binding of Gcr1 or the binding of other factors.…”
Section: Model Selectionsupporting
confidence: 74%
See 1 more Smart Citation
“…We also tried using different PWM models for Gcr1, which came from different experiments. None of these PWMs for Gcr1 are in good agreement with each other, nor do they agree well with our predictions (Harbison et al 2004;MacIsaac et al 2006;Pachkov et al 2007;Foat et al 2008;Spivak and Stormo 2012). The relationship between occupancy at the Gcr1 sites and the sites' effect on gene expression may be complicated by condition-specific binding of Gcr1 or the binding of other factors.…”
Section: Model Selectionsupporting
confidence: 74%
“…PWM models for TF binding (MacIsaac et al 2006;Pachkov et al 2007;Foat et al 2008;Spivak and Stormo 2012) were used to estimate the affinity of TFs to their cognate TFBSs. We used patser (Stormo et al 1982) to calculate these scores.…”
Section: Pwm Analysismentioning
confidence: 99%
“…The term "transfactome" is borrowed from [10] and is defined here as the compendium of proteins annotated as transcription factors (TF) in the GO. Only proteins expressed in a set of 254 GEPs from normal and tumor related human B cells were considered in the analysis (see 5.1).…”
Section: Resultsmentioning
confidence: 99%
“…The PWMs were converted to position-specific affinity matrices (PSAMs) and probe-TF affinities were calculated using the AffinityProfile utility in the MatrixREDUCE package as described previously [48]. The Pearson correlation between predicted affinity and MFE was then calculated.…”
Section: Methodsmentioning
confidence: 99%