Saccharomyces cerevisiae Transcription Factor Database
Names
More detailed information about this field from each metasource.
Saccharomyces cerevisiae Transcription Factor Database
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ScerTF
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
scertf
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
Names
More detailed information about this field from each metasource.
Saccharomyces cerevisiae Transcription Factor Database
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ScerTF
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
scertf
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
Names
More detailed information about this field from each metasource.
Saccharomyces cerevisiae Transcription Factor Database
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ScerTF
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
scertf
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
This source may no longer be available. No known URL could be resolved successfully.
ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.
Description
More detailed information about this field from each metasource.
ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Binding sites for Saccharomyces cerevisiae Transcription Factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
ScerTF catalogs over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
Webpage:
http://stormo.wustl.edu/ScerTF/Webpage
More detailed information about this field from each metasource.
http://stormo.wustl.edu/ScerTF/
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
http://stormo.wustl.edu/ScerTF
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: ScerTF Attribution requiredLicence name
More detailed information about this field from each metasource.
ScerTF Attribution required
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
More detailed information about this field from each metasource.
http://stormo.wustl.edu/ScerTF/
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species
PMID: 22140105
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
http://dx.doi.org/10.1093/nar/GKR1180
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species
PMID: 22140105
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
http://dx.doi.org/10.1093/nar/GKR1180
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species
PubMed citations: 44.
44 articles citing: ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species
Predicting which genes will respond to transcription factor perturbations. PMID:35666184
Cis-regulatory variants affect gene expression dynamics in yeast. PMID:34369376
Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast. PMID:33428627
Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross. PMID:33179598
Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data. PMID:33135076
The relation between crosstalk and gene regulation form revisited. PMID:32097416
Homotypic cooperativity and collective binding are determinants of bHLH specificity and function. PMID:31341088
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PMID:30897079
Intrinsic cooperativity potentiates parallel cis-regulatory evolution. PMID:30198843
Systematic Study of Nucleosome-Displacing Factors in Budding Yeast. PMID:30017582
Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization. PMID:30016330
Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry. PMID:29620524
Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding. PMID:29588420
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. PMID:29409522
Evidence for a hierarchical transcriptional circuit in Drosophila male germline involving testis-specific TAF and two gene-specific transcription factors, Mod and Acj6. PMID:29235675
Developmentally regulated internal transcription initiation during meiosis in budding yeast. PMID:29136644
Correspondence: DNA shape is insufficient to explain binding. PMID:28580956
Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators. PMID:27965290
Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast. PMID:27810962
Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae. PMID:27362276
The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast. PMID:27190003
Combinatorial Cis-regulation in Saccharomyces Species. PMID:26772747
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. PMID:26490019
Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast. PMID:26291518
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. PMID:26272984
Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification. PMID:25957495
Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation. PMID:25644834
The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. PMID:25477386
The Hsp90-dependent proteome is conserved and enriched for hub proteins with high levels of protein-protein connectivity. PMID:25316598
Transcription factor regulation and chromosome dynamics during pseudohyphal growth. PMID:25009286
A new exhaustive method and strategy for finding motifs in ChIP-enriched regions. PMID:24475069
Genetics of single-cell protein abundance variation in large yeast populations. PMID:24402228
Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data. PMID:24288374
Saccharomyces genome database provides new regulation data. PMID:24265222
Mot1 redistributes TBP from TATA-containing to TATA-less promoters. PMID:24144978
Mapping yeast transcriptional networks. PMID:24018767
Mapping the fine structure of a eukaryotic promoter input-output function. PMID:23955598
Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants. PMID:23921661
DNA motif elucidation using belief propagation. PMID:23814189
Mapping functional transcription factor networks from gene expression data. PMID:23636944
RAP: accurate and fast motif finding based on protein-binding microarray data. PMID:23464877
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis. PMID:23323883
Computational discovery of regulatory elements in a continuous expression space. PMID:23186104
Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data. PMID:23029415 - http://dx.doi.org/10.1093/nar/GKR1180
Tags:
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleotide
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
region
metasource: Fairsharing.org
version: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
gene regulation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:15.045032
Tags
More detailed information about this field from each metasource.
binding site
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleotide
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein domain
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
region
metasource: Fairsharing.orgversion: FAIRsharing.org: ScerTF; Saccharomyces cerevisiae Transcription Factor Database; DOI: https://doi.org/10.25504/FAIRsharing.qrv60a; Last edited: April 26, 2021, 3:58 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcription factors and regulatory sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
gene regulation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:35:15.045032
binding site nucleotide protein domain transcription region nucleic acid sequence transcription transcription factors and regulatory sites gene expression model organisms molecular interactions, pathways and networks gene regulation
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