A relational database that offers, in an organized and computable form, updated knowledge on transcriptional regulation in Escherichia coli K-12. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Major changes to the overall navigation and structure of the main pages have been made, offering more structured access to the data, based on the two dominant types of users: biologists, usually conducting individual search queries, and those interested in data collections.
A database of functional and evolutionary study of plant transcription factors. With the version 4.0, PlantTFDB offers 320 370 TFs from 165 species. Three types of annotation provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments, (ii) multiple types of regulatory elements identified from highthroughput sequencing data and (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements.
Provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. TRANSCompel contains data on eukaryotic transcription factors experimentally proven to act together in a synergistic or antagonistic manner.
A toolkit for the study of transcriptional regulation in plants. PlantRegMap provides a comprehensive, high-quality resource of plant transcription factors, regulatory elements and interactions between them. It contains sets of high-quality transcription factor binding motifs for 157 plant species, multiple types of regulatory elements derived from experiments, and genome-wide transcriptional regulatory interactions. In addition, multiple online tools are set up for transcription factor prediction, transcription factor binding site prediction, regulation prediction and functional enrichment analyses.
Covers motifs found in plant cis-acting regulatory DNA elements. PLACE contains some motifs in non-plant cis-elements in the hope that assist researchers in finding plant homologues. It offers functions allowing keyword search, signal scan search, or homology search in FASTA format. This database furnishes a brief definition and description of each motif, and relevant literature with PubMed ID numbers and GenBank accession numbers.
Provides data on enhancer control by transcription factors (TFs) and cofactors. Factors is a database that includes almost 470 TFs and more than 330 transcriptional cofactors (chromatin remodelers and modifiers and components of the basal transcription machinery) targeted to 24 contexts. Users can search for a specific protein or perform an advanced search with different features such as ortholog factors or cofactors.
Integrates several open access repositories of curated cis-elements, DNA motifs, and TFs into a unique repository. footprintDB systematically annotates the binding interfaces of the TFs by exploiting protein–DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition.
Provides information about gene regulation in prokaryotes. PRODORIC is a database that gathers DNA binding sites for prokaryotic transcription factors. This repository includes entries generated by manually screening the literature, as well as transcription factor binding site (TFBS) detected by diverse high-throughput techniques. The database provides a basis for the prediction of gene regulatory networks (GRNs). The web application Virtual Footprint, for recognizing DNA patterns in prokaryotic genomes, is also available, but only the most essential options are offered.
Gathers animal transcription factor (TF) lists, annotations, and provides prediction tools. AnimalTFDB is an animal TF database, which contains classification and annotation of genome-wide TFs and transcription cofactors in more than 90 animal genomes. The database provides annotations including gene phenotype and expression data in several species. TFs are classified into families, with one of them named “Others” including some orphan TFs. The prediction pipeline can be useful for TF identification in newly sequenced genome.
A database on composite elements. TRANSCompel focuses on so-called composite elements, consisting of two (or more) neighboring binding sites, characterized by synergistic or antagonistic effects between the two transcription factors binding to them. It contains, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based.
Provides information about transcription factor binding sites, as well as composite relationships within transcription factors. ooTFD based on data structures derived from the tables of the original database, now referred to as relational Transcription Factors Database (rTFD), which gathers information about the polypeptide interactions comprising and defining the properties of transcription factors.
Provides a set of hierarchical multi-layered concept of transcriptional regulation. CoryneRegNet consists of an ontology-based data warehouse. It employs a modular data processing pipeline that can recognize clusters of homologous proteins, match binding site motifs, determine operons and display special networks and graphs. This platform is useful for large-scale analysis of transcriptional regulation of gene expression in corynebacterial microorganisms.
Gathers data on more than 1700 transcriptions factors (TFs) related to Arabidopsis thaliana. AtTFDB is classified according to 50 families based on the presence of conserved domains. Searches can be made by browsing these families or by submitting a locus ID or a gene name. It displays a chart that give access to gene synonyms, nucleotide and protein sequences, information on related regulatory sub-network and links towards external pages such as The Arabidopsis Information Resource (TAIR). The complete database can be downloaded in zip format.
Provides a computational system adapted to genome annotation. rSNP_Guide includes both sequences of known Transcription Factors (TFs)-sites different types and available experimental data on alterations in binding of mutated DNA to unknown TFs. This resource focuses on the annotation of potential TF sites using models of experimentally characterized altered TF sites derived by rSNP_Guide system for recognizing TFs relevant to the known TF site.
A comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164 651 TCS proteins, from 2758 sequenced prokaryotic genomes. Several important new features have been added to P2CS since it was last described. Users can search P2CS via BLAST, adding hits to their cart, and homologous proteins can be aligned using MUSCLE and viewed using Jalview within P2CS. P2CS also provides phylogenetic trees based on the conserved signaling domains of the RRs and HKs from entire genomes.
Provides a portal dealing with Arabidopsis genes regulatory information. AGRIS is a repository composed of three mains panels (i) AtcisDB, that compiles upstream regions of annotated Arabidopsis genes; (ii) AtTFDB, that displays information on transcription factors (TFs); and (iii) GRG-X that allows users to browse among direct interactions between TFs and target genes. In addition, the platform provides links towards external resources.
Represents an integrated collaborative effort in neuroscience and psychiatry to collectively analyze genomic regulatory elements in a large cohort of well-curated human brains. Key goals of the PsychENCODE project are to provide an enhanced framework of regulatory genomic elements (promoters, enhancers, silencers and insulators), catalog epigenetic modifications and quantify coding and non-coding RNA and protein expression in tissue-and cell-type-specific samples from healthy (neurotypical) control and disease-affected post-mortem human brains.
Provides information about pathologically relevant mutations in transcription factor (TF) genes or in their binding sites (TFBS). PathoDB is a module of TRANSFAC, a database of TF and their DNA-binding sites and profiles. The database contains more than 10 530 transcription factor mutations and 19 mutated binding sites. It is searchable by diagnose methods, genotypes, mutated factors or sites and by phenotypes.
Collects information about transcription factors (TFs) in the fruit fly Drosophila melanogaster. FlyMine provides results from the curation of over 1052 candidate TFs selected for the presence of a canonical DNA-binding domain. The database allows users to search for a single gene of interest, upload extensive gene lists, from which the genes encoding TFs will be recognised and marked and make lists of TFs fulfilling specific criteria.
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.