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TranscriptomicsCurated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae transcription factors but a comprehensive eval...
ORGANISM(S): Saccharomyces cerevisiae 
2011-12-10 | E-GEOD-34306 | biostudies-arrayexpress
TranscriptomicsMolecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity
A subfamily of Drosophila homeodomain (HD) transcription factors (TFs) controls the identities of individual muscle founder cells (FCs). However, the molecular mechanisms by which these TFs generate unique FC genetic programs remain unknown. To investigate this problem, we first applied genome-wide ...
ORGANISM(S): Drosophila melanogaster 
2012-01-28 | E-GEOD-35380 | biostudies-arrayexpress
TranscriptomicsHighly parallel assays of tissue-specific enhancers in whole Drosophila embryos
Understanding transcriptional regulatory networks requires the identification and characterization of cis-regulatory modules (CRMs), DNA sequences which can direct expression of associated genes to a specific cell type and/or developmental stage. Reporter assays for the capacity of a candidate CRM ...
ORGANISM(S): Drosophila melanogaster 
2013-07-13 | E-GEOD-41503 | biostudies-arrayexpress
TranscriptomicsEvaluation of methods for modeling transcription factor sequence specificity
Genomic analyses often involve scanning for potential transcription-factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein’s binding specificity by representing sequence motifs, including the gaps a...
ORGANISM(S): synthetic construct 
2012-12-13 | E-GEOD-42864 | biostudies-arrayexpress
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