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TranscriptomicsA computational genomics approach to identify cis-regulatory modules - a case study using E2F1
We first trained a set of experimentally identified E2F1 targets by a ChIPModules approach, the identified module of E2F1 and AP-2alpha was validated by ChIP-chip assays. We have performed 3 sets of ChIP-chip experiments in MCF-7 for E2F1 and AP-2alpha respectively. The common genes bound by both E2...
ORGANISM(S): Homo sapiens 
2010-07-01 | E-GEOD-5175 | biostudies-arrayexpress
TranscriptomicsE2F in vivo binding specificity: comparison of consensus vs. non-consensus binding sites
Recent genome-scale ChIP-chip studies of transcription factors have shown that a low percentage of experimentally determined binding sites contain the consensus motif for the immunoprecipitated factor. In most cases, differences between in vivo target sites that contain or lack a consensus motif ha...
ORGANISM(S): Mus musculus 
2008-10-01 | E-GEOD-12126 | biostudies-arrayexpress
TranscriptomicsA ChIP-chip analysis of E2F family in normal and tumor cells reveals interchangeable roles of E2F family members
Using ChIP-chip assays, we examined the binding patterns of three members of E2F family in five different cell types. Keywords: ChIP-chip We used ENCODE arrays to determine the loaction of E2F family, then identify their binding motifs in vivo. We used promoter arrays to assess the relationship of E...
ORGANISM(S): Homo sapiens 
2007-08-22 | E-GEOD-8716 | biostudies-arrayexpress
TranscriptomicsUsing ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
We compared 12 different cell populations, including embryonic stem cells before and during differentiation into embryoid bodies as well as various types of normal and tumor cells to determine if pluripotent vs. differentiated cell types use different mechanisms to establish their transcriptome. We ...
ORGANISM(S): Mus musculus 
2008-03-31 | E-GEOD-10504 | biostudies-arrayexpress
GenomicsGenome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome.
Previous studies of E2F family members have suggested that protein-protein interactions may be the mechanism by which E2Fs are recruited to specific genomic regions. We have addressed this hypothesis on a genome-wide scale using ChIP-seq analysis of MCF7 cell lines that express tagged wildtype and m...
ORGANISM(S): Homo sapiens 
2011-04-04 | E-GEOD-28286 | biostudies-arrayexpress
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