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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.

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.

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.

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.

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.

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.

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.

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.

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.

PathoYeastract / PATHOgenic YEAst Search for Transcriptional Regulators And Consensus Tracking

An information system for analyzing and predicting transcription regulatory associations at the gene and genomic levels in the pathogenic yeasts candida albicans and candida glabrata. PathoYeastract offers a complete integration of all this experimentally validated transcriptional regulatory data. This database includes 28 000 unique documented regulatory associations between transcription factors (TF) and target genes and 107 DNA binding sites, considering 134 TFs in both species.

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.

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.

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.

CistromeMap

A comprehensive and consistently annotated knowledgebase of all published or public ChIP-seq and DNase-seq data in mouse and human. In total, there are 2711 ChIP-Seq datasets for transcription and chromatin regulators, 2355 for histone modifications and variants, 412 DNase-Seq and 996 control datasets. Among transcription and chromatin regulators, POLR2A, CTCF, ESR1, RELA and EP300 are the most often profiled ChIP-Seq factors. For histone marks, H3K4me3, H3K27me3, H3K4me1, H3K36me3 and H3K9me3 ChIP-Seq are the most common, which together accounts for over 70% of all of the histone ChIP-Seq data.

STIFDB / Stress Responsive Transcription Factor Database

Provides a database of abiotic stress responsive genes. STIFDB is a resource that analyses promoters of abiotic stress responsive genes for potential stress-specific transcription factor binding sites. This resource can provide insights into the regulation of these stress responsive genes by upstream transcription factors. It also offers clues towards stress signal that affects the transcription of this gene, which might offer clarity about signal specific regulation.

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.

YPA / Yeast Promoter Atlas

Obsolete
Collects promoter features in Saccharomyces cerevisiae. YPA integrates resources such as transcription start sites (TSSs), TATA boxes, transcription factor binding sites (TFBS), nucleosome occupancy, DNA bendability, transcription factor (TF)-TF interaction, and gene expression data. The database provides an interface for browsing the yeast genome and viewing multiple promoter features simultaneously. Users can retrieve the data collected from various sources.

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.

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.

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.

DPTF / Database of Poplar Transcription Factors

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.