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TranscriptomicsHuman skeletal muscle differentiation time course
We have developed an algorithm (“Lever”) that systematically maps metazoan DNA regulatory motifs or motif combinations to the sets of genes that they likely regulate. Lever accomplishes this by assessing whether the motifs are enriched within cis regulatory modules (CRMs), predicted by our “Ph...
ORGANISM(S): Homo sapiens 
2010-06-25 | E-GEOD-4460 | biostudies-arrayexpress
TranscriptomicsA Transcriptional Signature and Common Gene Networks Link Cancer with Metabolic Syndrome and Auto-immune Diseases
Epidemiological studies have revealed concurrence of specific cancers with other disease states such as metabolic syndrome, inflammatory disease and autoimmune disease. Patients with these chronic conditions have a higher incidence of various cancers, more aggressive tumors, and a higher mortality r...
ORGANISM(S): Homo sapiens 
2010-04-19 | E-GEOD-17941 | biostudies-arrayexpress
GenomicsIntegrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network
Contemporary high throughput technologies permit the rapid identification of transcription factor (TF) target genes on a genome-wide scale, yet the functional significance of TFs requires knowledge of target gene expression patterns, cooperating TFs and cis-regulatory element (CRE) structures. Here...
ORGANISM(S): Drosophila melanogaster 
2012-11-13 | E-GEOD-38402 | biostudies-arrayexpress
TranscriptomicsVariation in homeodomain DNA-binding revealed by high-resolution analysis of sequence preferences
Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise DNA-binding specificities. We determined the binding preferences of the majority (168) of mouse homeodomains to all possible 8-base sequences, re...
ORGANISM(S): Mus musculus 
2010-06-26 | E-GEOD-11239 | biostudies-arrayexpress
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
ProteomicsGenomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (validation)
DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs wi...
ORGANISM(S): Saccharomyces cerevisiae 
2013-03-29 | E-GEOD-44437 | biostudies-arrayexpress
ProteomicsGenomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (different concentrations)
DNA sequence is a major determinant of the binding specificity of transcription factors (TFs) for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs wi...
ORGANISM(S): Saccharomyces cerevisiae 
2013-03-29 | E-GEOD-44436 | biostudies-arrayexpress
TranscriptomicsDistant cis Regulation of Myogenic Differentiation
Identifying tissue and condition-specific gene regulatory elements and the mechanisms by which they associate with their target genes in human cells remains a significant challenge, largely due to the vast amount of non-protein-coding sequence in the human genome. Despite increasing evidence of phys...
ORGANISM(S): Homo sapiens 
2012-02-01 | E-GEOD-29865 | 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
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