Kolchanov, N., Ignatieva, E., Podkolodnaya, O., et al., Transcription Regulatory Region Database (TRRD): A Source of Experimentally Confirmed Data on Transcription Regulatory Regions of Eukaryotic Genes, Bioinformatics of Genome Regulation and Structure II , Kolchanov, N., Hofestaedt, R.,...
Transcription Regulatory Regions Database (TRRD) has been developed for accumulation of experimental information on the structure–function features of regulatory regions of eukaryotic genes. Each entry in TRRD corresponds to a particular gene and contains a description of structure–function features of ...
Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind ...
Specific sequences in the genome are recognized by regulatory proteins, which can induce or repress transcription. These regions are known asresponse elements. Among a series of regulators, many hormones act as modulating response elements in DNA. In the case ofrepressor proteins, binding to DNA ...
Of particular interest are interactions in which a given TF regulates other TFs; these interactions define the TF regulatory networks (TRNs) that underlie cellular identity and major function. Chromatin accessibility depicts whether or not a DNA sequence is physically accessible and provides a direct ...
We hypothesized that there exist systematic differences in TF regulatory decay distances between active and repressed genomic regions. Having defined A-type and B-type TADs with high and low H3K27ac marks, respectively (Fig. 2a), we examined whether regulatory distances differ between these TAD ...
The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques tha...
TcoFBase curated 2322 TcoFs and 6759 TcoFs associated ChIP-seq data from over 500 tissues/cell types in human and mouse. Importantly, TcoFBase provided detailed and abundant (epi) genetic annotations of ChIP-seq based TcoF binding regions. Furthermore, TcoFBase supported regulatory annotation ...
Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements...
By doing this, SoyDB can be linked with other soybean genome annotations. Furthermore, we may identify the binding regions on the soybean DNA sequences, which can further help biologists target the regulated regions on soybean genome. Conclusions SoyDB is a comprehensive database for soybean ...