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RegulonDB
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.
PLACE
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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.
PlantRegMap
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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.
PlantTFDB / Plant Transcription Factor Database
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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.
footprintDB
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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.
PRODORIC / PROcariotIC Database Of Gene-Regulation
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.
DBTSS / DataBase of Transcriptional Start Sites
It was originally constructed as a collection of uniquely determined transcriptional start sites (TSSs) in humans and some other species in 2002. Since then, DBTSS has been regularly updated and in recent updates epigenetic information has also been incorporated because such information is useful for characterizing the biological relevance of these TSSs/downstream genes. DBTSS is no longer a mere storage site for TSS information but has evolved into an integrative platform of a variety of genome activity data.
AGRIS / Arabidopsis Gene Regulatory Information Server
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.
P2CS
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.
PsychENCODE
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.
CTCFBSDB
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.
EPDnew
A recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been described in more detail in a previous NAR Database Issue. EPD is an old database of experimentally characterized eukaryotic POL II promoters, which are conceptually defined as transcription initiation sites or regions. EPDnew is a collection of automatically compiled, organism-specific promoter lists complementing the old corpus of manually compiled promoter entries of EPD. This part is exclusively derived from next generation sequencing data from high-throughput promoter mapping experiments.
Tractor_DB
Provides data of computationally predicted regulatory interactions within the genomes of several organisms of this group. Tractor_DB contains orthology relationships between gene pairs that are constructed with the bidirectional best hits (BBH) methodology. It permits the user to directly retrieve the information regarding the conservation of regulatory interactions within a given regulon from a map that contains all known Escherichia coli transcription factors (TFs) and the regulatory interactions that interconnect them.
TcoF-DB / Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins
A database for human transcription co-factors and transcription factor interacting proteins. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice.
PlnTFDB / Plant Transcription Factor Database
Compiles data relative to putatively complete sets of transcription factors (TFs) and transcriptional regulators (TRs) from 19 plant species. PInTFDB is a repository with the aim of determining and recording plant genes involved in transcriptional control. It provides information about the different regulatory proteins and their classification into families, sequence alignments, as well as literature references and links to other databases.
AtTFDB / Arabidopsis transcription factor database
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.
YEASTRACT / Yeast Search for Transcriptional Regulators And Consensus Tracking
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.
FlyFactorSurvey
A database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. FlyFactorSurvey provides community access to over 400 recognition motifs and position weight matrices for over 200 TFs, including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. Together, this database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences.
PlantProm / Plant Promoter database
Offers promoter data collecting procedure and specific features of plant promoter sequences. PlantProm DB serves as a learning set in developing plant promoter prediction programs. It provides information on plant promoters with experimentally known transcription start site (TSS): (i) DNA sequence of the promoter region, (ii) Nucleotide Frequency Matrices (NFM) for canonical promoter elements, (iii) taxonomic and promoter type classification of promoters.
FlyTF / Transcription factor datamine for Drosophila melanogaster
Collects information about transcription factors (TFs) in the fruit fly Drosophila melanogaster. FlyTF 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.
MachiBase
Gives access to Drosophila melanogaster 5’-end mRNA tags at different developmental states. MachiBase is designed to assist fly biologists in their analyses of gene expression and in placing expression data in the context of functional genomics through genomic orientation. Users can access information on differentially expressed genes by either inputting the gene name as a keyword or selecting a chromosomal location. The database can assist biologists in explaining transcriptional initiation mechanisms by combining additional information on chromatin structure and DNA methylation.
DPRP / Database of Phenotype-specific Regulatory Programs
Facilitates the search and application of gene expression data for generating new hypotheses on transcriptional regulatory programs under diverse biological and clinical contexts. DPRP contains about 980 gene expression data sets, which include about 29 750 samples. Users can search a disease concept to discover all related gene expression data sets, choose the interested data set and then select a subset pair within the data set for transcription factor (TF) regulatory program analysis.
CR Cistrome / Chromatin Regulator Cistrome
A ChIP-seq database containing information on chromatin regulators (CRs) and CR-histone modification (HM) linkages in human and mouse, and it comprises all qualified CRs with available public ChIP-seq data, manually curated information on these CRs, including their full names, aliases, introductions, functions, known disease associations and CR type as well as the ChIP-seq data analysis results. This database also provides related HMs’ ChIP-seq data analysis and CR-HM linkage analysis results for readers, writers and erasers in cases where there are available HM ChIP-seq data collected under the same condition as the associated CRs. Each CR could be linked to NCBI, UniProt, Wikipedia and GeneCards to provide user alternative information.
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