Tag: transcription

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxo ...

The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements ...

Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which ...

The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually cur ...

Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 5 ...

The Swissregulon Database contains genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including i) Experimentally determined binding sites reported in the li ...

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transc ...

HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v10 provides transcription factor (TF) binding models for 601 human and 396 mouse TFs. In addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides a set of dinucleotide ...

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins.

RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In t ...

This database includes TSS data from adult and embryonic human tissue. DBTSS now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures.

Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activit ...

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

SignaLink is an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. it allows browsing of signaling pathways, cross-talks and multi-pathway proteins; selection of transcriptional, post- ...

REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence ...

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regula ...

SEA (Super-Enhancer Archive) is a web-based comprehensive resource focusing on the collection, storage and online analysis of super-enhancers. It focuses on integrating super-enhancers in multiple species and annotating their potential roles in the r ...

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

TransmiR is a database for transcription factor-microRNA regulations, which is free for academic usage.

The Human Transcriptional Regulation Interactions database (HTRIdb) is a repository of experimentally verified interactions among human transcription factors (TFs) and their respective target genes. It has been constructed to be an open-access and us ...

The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.

PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR ...

Gene Transcription Regulation Database (GTRD) is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse.

This resource provides information primarily on the upstream non-coding sequence data of genes in 3 genomes which gives insight into the transcription factors binding sites (TFBSs). For each transcript, the region scanned extends from 10,000bp upstre ...

dbSUPER is the first integrated and interactive database of super-enhancers, which contains 82234 super-enhancers in 102 human and 25 mouse tissue/cell types.

Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.

The database of Disease-Gene Associations with annotated Relationships (eDGAR) is a database for collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar. For each heterogeneous or polygenic disease, ...

CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain. It aims at becoming a reference, highly-accessed database by relying on its ability to customize navigation and data extraction, its relevance to the communit ...

ReMap is an integrative analysis of transcription factor ChIP-seq experiments publicly available, merged with the Encode dataset. The resource is an extensive regulatory catalogue of transcription factor binding sites from transcription factors (TFs) ...

Predicted regulons in prokaryotic genomes

Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phyloge ...

Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved tran ...

The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of informa ...

Genome-wide plant promoter database for several plant species, including Arabidopsis thaliana, rice, poplar, and Physcomitrella patens.

The TFClass Schema is an identifier schema for classifying transcription factors according to a six-level schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene ...

ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accu ...

DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF incl ...

ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.

WebGesTer Database (DB) is the largest compilation of intrinsic terminators of transcription. It comprises of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. The database is the storehouse for algorithm ...

Coexpressed genes and networks in human and mouse

FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified T ...

Database for Human Transcription Co-Factors

Estimates of DNA-binding specificity for protein-DNA complexes in PDB

ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 ...

EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.

DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. Based on the Arabidopsis thaliana and Homo sapiens genome annotation, this resource is also a ...

GenomeTraFaC is a database of conserved regulatory elements obtained by systematically analyzing the orthologous set of human and mouse genes. It mainly focuses on all of the high-quality mRNA entries of mouse and human genes in the Reference Sequenc ...

TFBSshape provides DNA shape features for transcription factor binding sites (TFBSs) that in addtion to sequence features, usually in the form of position weight matrices (PWMs), characterize DNA binding specificities of transcription factors (TFs) f ...

EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcript ...

If a database is inadequate in terms of its description, unclear with respect to the terms of use, or is not downloadable, it may not be fully used, cited or rightly acknowledged by the (research) communities. This is even true for databases with hig ...

REGULATOR is a metazoan transcription factor (TF) and maternal factor resource, specifically designed for developmental biology studies. Maternal factors were expressed in unfertilized eggs, and gradually reduced as time goes on. In order to reduce t ...

DBD provides transcription factor predictions for more than 150 completely sequenced genomes available for browsing and download. Predictions are based on presence of sequence specific DNA binding domain assignments using hidden Markov models from th ...

Transcriptional regulatory element database

Transcription factor database

Human transcription factor binding data from ChIP-seq

Yeast Transcription Factor binding Site sequence Collection

TESS (Transcription Element Search System, http://www.cbil.upenn.edu/tess) is a web-based service that searches DNA sequence for transcription factor binding sites. It integrates three databases of transcription factors and binding site models, and p ...

Drosophila melanogaster 5' mRNA transcription start site database

Regulatory SNPs affecting predicted transcription factor binding sites

DNA-binding specificities of transcription factors in Drosophila

Transcription factor binding site sequences obtained using high-throughput SELEX method

A database of phenotype-specific regulatory programs derived from transcription factor binding data

Transcription factor binding profiles deduced from ChIP-seq or ChIP-chip data

Transcription factor binding profiles in human haematopoietic stem/progenitor cells

The PReMod database describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide/ ...

Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, Transcription Factors (TFs), TFs' binding sites, operons) within its genome. As more genomes of ...

The TRANSFAC® database has been constructed to model the interaction of eukaryotic transcription factors with their DNA-binding sites and how this affects gene expression. At its core are the three tables FACTOR, SITE, and GENE. A link between FACTOR ...

Triplex Target DNA Sites in the human genome

Various genes get upregulated in plants during adverse environmental conditions, which alter the metabolic functions to mitigate the stress effects for adaptation. Therefore, it is important to know the regulatory motifs of stress-induced genes for g ...

TRANSPATH® is a database on signal transduction pathways that are modeled as bipartite graphs with molecules and reactions as node classes [1,2,3,4,5]. The molecule entries include polypeptides, modified forms, multicomponent complexes, high-order ab ...

Computational models for gene silencing in C. elegans

G-quadruplex motifs and potentially G-quadruplex regulated genes

ChIPBase v2.0 is an open database for studying the transcription factor binding sites and motifs, and decoding the transcriptional regulatory networks of lncRNAs, miRNAs, other ncRNAs and protein-coding genes from ChIP-seq data. Our database currentl ...

Experimentally identified and predicted CTCF binding sties

Plant promoter sequences

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a col ...

A database of yeast promoters

The TRANSCompel® database is devoted to the particular aspect of gene transcriptional regulation [1-7]. It contains information about composite elements - the basic structures of combinatorial gene regulation [7]. Composite regulatory elements consis ...

ooTFD (1) is a database of transcription factors maintained in object-oriented and object-relational database systems. There are, at the time of this writing, about 7500 TF binding sites entries in this database, from both prokaryotic and eukaryotic ...

Stress-responsive gene in various plant species

The Comparative RNA Web (CRW) Site disseminates information about RNA structure and evolution that has been determined using comparative sequence analysis. We present both raw (sequences, structure models, metadata) and processed (analyses, evolution ...

TiProD is a database of human promoter sequences for which some functional features are known. It allows a user to query individual promoters and the expression pattern they mediate, gene expression signatures of individual tissues, and to retrieve s ...

SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for these oligomers recognition. In vitro selection of oligomers binding target proteins is a novel technology inte ...

The NCI and NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH), which are complementary fluor ...

ACTIVITY, a database on DNA site sequences with known activity magnitudes, measurement systems and sequence-activity relationships under fixed experimental conditions is additionally adapted to applications to the phylogenetic footprints of known sit ...

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways, and kinetic characteristics of elementary processes. In the past two years, the GeneNet structure was considerably im ...

ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution process (mainly by means of phage display technique). ASPD database is being compiled b ...