Simplifies the studies on insulators and their roles in demarcating functional genomic domains. CTCFBSDB is an online database that includes almost 15 million experimentally determined CTCF binding sites across several species. This repository contains several features: (1) inclusion of genomic topological domains defined using Hi-C data; (2) identification of CTCF-binding sequences that overlap a given CTCF-binding sequence; (3) inclusion of occupancy data; (4) classification of motif match type; and (5) integration with Genome Browser.
Enables an interactive global view of genomic scale regulatory networks. YEASTRACT integrates several experimentally validated transcriptional regulatory data for published S. cerevisiae. This resource contains more than 41 000 regulatory associations based on DNA binding evidence and about 172 000 on expression evidence. It holds analysis tools for investigation of the transcriptional regulation of genes involved in a particular biological response.
A database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries.
Compiles regulatory sites annotations for 18 organisms. SwissRegulon deals with both prokaryotes and eukaryotes and furnishes information about position-specific weight matrices (WMs), promoters and predictions of transcription factor binding sites (TFBSs), curated from literature or derived from experiments. Users can explore annotations for promoters, genes or regulators of interest or download data of interest into a flat format file.
A plant transcription factor (TF) database containing 2576 putative poplar TFs distributed in 64 families. These TFs were identified from both computational prediction and manual curation. We have provided extensive annotations including sequence features, functional domains, GO assignment and expression evidence for all TFs. In addition, DPTF contains cross-links to the Arabidopsis and rice transcription factor databases making it a unique resource for genome-scale comparative studies of transcriptional regulation in model plants.