Tag: transcription factors and regulatory sites

The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and expe ...

The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

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 ...

Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignm ...

NeuroMorpho.Org is a centrally curated inventory of 3D digitally reconstructed neurons associated with peer-reviewed publications. The goal of NeuroMorpho.Org is to provide dense coverage of available reconstruction data for the neuroscience communit ...

FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.

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 ...

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

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 ...

Detects this family of direct repeats found in the DNA of many bacteria and archaea.

This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...

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 ...

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.

The Ribosomal Database Project - II (RDP-II)(1) provides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, anal ...

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 ...

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated Microbial Signal Transduct ...

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 ...

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 ...

The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arab ...

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 ...

RNA-binding proteins and their specificities

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.

The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and anno ...

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

FuzDB compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database ha ...

Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, di ...

A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database ...

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 ...

Gypsy database of mobile genetic elements

Predicted regulons in prokaryotic genomes

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

The Open Data Commons for Traumatic Brain Injury (DC-TBI) was created by the TBI community to mitigate dark data in TBI research. The ODC-TBI also aims to increase transparency with individual-level data, enhance collaboration, facilitate advanced an ...

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 ...

POcket Similarity Search Using Multiple-Sketches (PoSSuM) includes all the discovered protein-small molecule binding site pairs with annotations of various types (e.g., UniProt, CATH, SCOP, SCOPe, EC number and Gene ontology). PoSSuM enables rapid ex ...

Experimentally-determined binding sites of RNA-binding proteins

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, a ...

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 ...

Gene regulation in bacteriophages

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 ...

circAtlas is an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-dept ...

Database for Human Transcription Co-Factors

Indel Flanking Region Database is an online resource for indels (insertion/deletions) and the flanking regions of proteins in SCOP superfamilies. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid indels, substitut ...

Next-generation sequencing single-cytosine-resolution DNA methylation data

Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon red ...

Database of Human Lung Cancer Research

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene e ...

Curated compendium of specific DNA-binding RNA polymerase II transcription factors.

HMM-based Identification of TF Footprints

A database of phosphorylation-related SNP (phosSNP) which are non-synonymous SNP (nsSNP) that affect the protein phosphorylation status. Using an in-house developed kinase-specific phosphorylation site predictor (GPS 2.0), we computationally detected ...

The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies.

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 ...

Hydrogen/deuterium exchange data on protein folding and stability

Reference human lncRNA sets

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, a ...

Dragon Database of Genes Implicated in Prostate Cancer is a knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). DDPC provides gene-associated data such as protein annotation, molecular pathways, ontologies and trans ...

An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Table of Multiplexed Assay of Variant Effect (MAVE) studies. MaveDB - A repository for MAVE assay datasets. To cite this document, please use the c ...

a database of endothelial cell transcriptomics data. EndoDB The endothelial cell database (EndoDB) is a freely accessible added-value database that facilitates bench scientists to unlock the untapped potential of publicly available (single cell) tra ...

EXPath is a database resource that collects and utilizes expression profiles derived from microarray under various conditions to infer metabolic pathways for six model plants: Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycin ...

Database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. It provides an interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to valida ...

Mutations in Ligand Binding Sites gene DataBase

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionisation equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play ...

UK PubMed Central is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. Now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent bio ...

Curated database to annotate gene promoters identified from ChIP-seq results. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, ...

Database of zinc binding sites.

Deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Search by RsID, Gene, Region or Disease:. Links MeT-DB Whistle DRUM DRRMSDB. A database for the disease-associated genetic variants tha ...

Database of genetic variations associated with long noncoding genes.

a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resour ...

Human Assay-for-Transposase-Accessible Chromatin data

Annotated reference dataset for transcriptional start sites (TSS) in human and mouse.

A system of databases documenting the influence of mutations in regulatory gene regions.

FORK-seq is a replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL ...

Complex Carbohydrate Magnetic Resonance Database (CCMRD) is a solid-state NMR database for complex carbohydrates. Carbohydrates play key roles in many life activities in living organisms. As an emerging technique with steadily improving resolution, s ...

G-quadruplex Ligands Database

anti-CRISPR operons

EpiRegio is a resource of Regulatory EleMents (REMs) associated to protein coding, and non-protein coding genes. For a detailed documentation, please read our documentation.

DESSO is a deep learning-based framework that can be used to accurately identify both sequence and shape regulatory motifs from the human genome.

Database to discover the regulate relationships in the context of enhancers.

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.

FuncPEP is a database of functional peptides encoded by non-coding RNAs.

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.

a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. RNAactDrug a comprehensive database of RNAs associated with Drug sensitivity from multi-omics data. RNAactDrug is a comprehensive resource for querying associa ...

Tissue-specific circRNA expression profiles and regulatory networks

3DSNP is a database for comprehensively annotating the regulatory function of human noncoding SNPs by exploring their 3D interactions with genes and genetically associated SNPs mediated by chromatin loops. 3DSNP integrates Hi-C data together with a v ...

Database of enhancers identified by high-throughput reporter assays.

a tool for analyzing putative transcription factor binding sites in salmonid genomes | SalMotifDB: cis-regulatory motif database for salmonids | We're getting there, it's worth the wait

TarDB is a database for conserved miRNA targets, degradome supported miRNA targets and miRNA-triggered phasiRNAs in plants. TarDB is a plant miRNA target repository, which is based on cross-species conservation filter, degradome PARE-seq, and small R ...

An Integrative De Novo Variant Knowledge Base for Developmental Disorders. NeuroPsychiatric Mutation Knowledge Base. Welcome to our open access database PsyMuKB. PsyMuKB is a comprehensive knowledge base that links transcriptional and translationa ...

A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. A high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosom ...

A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.

A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.

The Hormone Receptor Target Binding Loci, HRTBLDb database contains hormone receptor binding regions (binding loci) from in vivo ChIP-based high-throughput experiments as well as in silico, computationally predicted, binding motifs and cis-regulatory ...

An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma.

A knowledgebase of lncRNA function in human cancer.

Regeneration Roadmap aims to compile large datasets for gene expression and regulation created by a broad spectrum of high-throughput omics technologies. This one-stop service provides user-friendly functionalities to explore annotated regeneration-r ...

A comprehensive database for decoding the regulatory transcription co-factors in human and mouse.

TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.

ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease.

YEASTRACT+ combines the existing database information of all yeast species, providing bioinformatics tools for the prediction and visualization of gene and genomic regulation based on orthologous regulatory associations described for other yeast spec ...

m6ADD is a database containing manually collected experimentally confirmed m6A (N6-methyladenosine)-disease data and data obtained from high-throughput disease m6A modification profiles, aimed at exploring the association between m6A modified gene di ...

FGviewer is an online visualization tool for functional features of human fusion genes. FGviewer is aiming for the effective visualization of the functional features of fusion genes for better prioritization of therapeutic target selection. FGviewer ...

Database of Dna REgulatory Motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples.

A manually curated database of experimentally determined dNTP pools and pool changes in biological samples.

Integrated multi-omics database of human and mouse early embryo.

A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain.

An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis.

The database provides single-cell enhancer annotation in three species, including human (hg19), mouse (mm9), and fly (dm3).

CONREL is a genome browser that allows for the exploration of consensus regulatory elements at different levels of abstraction. The total binding affinity of transcription factors on whole consensus region sequences is here fully exploited to charact ...

RNAPhaSep is a novel database that collects phase separation related RNAs manually curated from publication and public databases. Various properties of RNAs together with the corresponding phase separation conditions validated by experiments were col ...

database of traits of fish to promote advances in fish aquaculture. toff-project – Database of Traits OF Fish. TOFF (i.e. Traits OF Fish) is a curated database focusing on functional trait information for fish that aims at bringing together behavio ...

A database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Cancer hallmarks rely on its specific transcriptional programs, which are dysregulated by multiple mechanisms, including genomic aberrations in the DN ...

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 ...

Cancer drivers at non-coding regions

A comprehensive database for regulations of human transcription factors and their targets. Transcription factors (TFs) as key regulators could modulate the expression of target genes by binding to specific DNA sequences of their promoter(s) or enhan ...

ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them.

Haloarchaeal genomes database.

T1TAdb is a database of Type I Toxin-Antitoxin systems.

CancerCRCdb is a comprehensive database of human core regulatory circuitry.

A positive miRNA-target regulations database.

Gateway to publicly accessible CRISPRs database.

A Knowledgebase of RAG Regulators.

A comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human.

A comprehensive enrichment analysis software for human genomic regions.

Database of cooperating miRNAs and their mutual targets which enables researchers explore novel patterns in gene regulation.

An integrated resource for human miRNA-Transcription Factor-Target Gene coregulatory networks and associated Feed Forward Loops. Defence Institute of Physiology and Allied Science. miRNA and Transcription Factors (TFs) are fundamental transcription ...

A PROkaryotic Chromatin ImmunoPrecipitation DataBase

A database for comparative co-expression networks analysis of allohexaploid wheat and its progenitors.

A Database for Comparing Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.

A database of enhancer mediated feed-forward loops for human and mouse.

A comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation.

A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.

HORDB a comprehensive database of peptide hormones.

A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem.

A comprehensive database for alternative splicing in tea plants (Camellia sinensis).

Fuzzle 2.0 is a database of evolutionary related protein fragments.

ERMer: A serverless platform for navigating, analyzing, and visualizing Escherichiacoli regulatory landscape through graph database.

TFcancer is a manually curated database of transcription factors associated with human cancer. TFcancer features in comprehensive annotations of TFs in human cancers. TFcancer mainly focused on the influence of transcription factors on four dimension ...

A universal platform for annotating and analyzing non-classically secreted proteins of Gram-positive bacteria

BoMiProt is a manually curated, comprehensive repository of published information of bovine milk proteins.

REVA as a Well-curated Database for Human Expression-modulating Variants.

CpGmotifs is a tool to discover DNA motifs associated to CpG methylation events.

A dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development.

Black Pepper Drought Transcriptome Database (BPDRTDb) catalogues all the genomic information like differential expressed genes, microsatellites, variants, transcriptional factors, pathways, domain and families of assembled transcriptome associated wi ...

ZebraShare is intended to help establish fruitful collaborations by sharing mutant fish lines, and information about these mutants, particularly when authors do not otherwise see a clear path to publication.

A database of polar amylodogenic peptides from disordered proteins.

A comprehensive animal enhancer RNA database.

proMGE is a resource for the retrieval of 6 Mobile Genetic Element (MGE) categories in 76K genomes (totalling to 2.4 million prokaryotic MGEs) and classification of new ones in user provided protein sequences from genomes and genomic fragments.

Database which collects human and mouse embryonic stem cell related datasets. These datasets cover perturbation (both knock-down and overexpression) and chromatin immunoprecipitation (ChIP) experiments in embryonic stem (ES) and carcinoma (EC) cell l ...

A Database of Regulatory SNPs for Agricultural Animal Species.

Metal binding sites, antigen epitopes, and drug binding sites are viral protein hotspots that control how viruses interact with their hosts. Like Google maps organizes and annotates points of interest on the planet, virus-M-E-D (Metal binding sites, ...

Here, we have predicted CasRx guide efficiency for all human and mouse RefSeq genes. We have also enabled custom sequence input for CasRx guide design.

CATA (The chromatin accessibility of cancer database) is a comprehensive Cancer ATAC-seq database that aim to provided a large number of available resources on cancer ATAC-seq datas. The database was annotated with potential functions of ATAC-Peak in ...

OlfactionBase is a manually-curated comprehensive database that incorporates multidimensional facets of major components involved in the olfaction process, i.e., odors, chemicals (both odorants and odourless), Olfactory Receptors (ORs), odorant-OR in ...

A framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing. Genomic Regulatory Elements ENcyclopedia. This is the home of the GREEN-DB and companion tools (GREEN-VARAN). Genomic Regulatory Elemen ...

VaximmutorDB is database for vaccine immune factors. A "vaximmutor" is coined here to represent an immune factors that is triggered by a vaccination and plays a role in vaccine-induced host immunity. Vaximmuntors are specifically targeted by the inna ...

A database storing SNPs and their predicted impact on transcription factor (TF) binding in promoter regions for different crops.

Color Data is a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets. Color Data is the largest public database of its kind, containing aggregated genetic and phenotypic information from 54,000 ...

This Data Coordination Center web page allows DANIO-CODE consortium members to submit and view their data sets annotated with standard metadata nomenclatures.

FABRIC Cancer Portal is a comprehensive catalogue of human coding genes in cancer based on the FABRIC framework. FABRIC quantifies the selection of genes in tumor and weighs their evidence for being cancer drivers.

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products. decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER). Alexander M. Kloosterman, Peter Cimermancic, Somayah S. Elsayed, Chao ...