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Cis-regulatory DNA element databases | Genome annotation

Transcription factors (TFs) influence gene expression by binding to specific cis-acting elements in a genomic sequence. Thus, accurate models for describing the binding properties of TFs are essential in modeling transcription. From a set of known…
JASPAR
Dataset

JASPAR

An open-access database storing curated, non-redundant transcription factor…

An open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple…

AthaMap
Dataset

AthaMap

Generates a map of predicted transcription factor binding sites (TFBS) and…

Generates a map of predicted transcription factor binding sites (TFBS) and small RNA target sites for the whole Arabidopsis thaliana genome. AthaMap can be used for bioinformatic predictions of…

TRANSFAC
Dataset

TRANSFAC

Provides data on eukaryotic transcription factors, their experimentally-proven…

Provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. TRANSCompel contains data…

DBTSS
Dataset

DBTSS DataBase of Transcriptional Start Sites

It was originally constructed as a collection of uniquely determined…

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…

HOCOMOCO
Dataset

HOCOMOCO HOmo sapiens COmprehensive MOdel COllection

Contains transcription factor (TF) binding models obtained by careful…

Contains transcription factor (TF) binding models obtained by careful integration of data from different sources. HOCOMOCO v10 contains non-redundant curated binding models for 601 human and 396…

UniPROBE
Dataset

UniPROBE Universal PBM Resource for Oligonucleotide Binding Evaluation

Serves as a convenient source of information on published data generated using…

Serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding…

CIS-BP
Dataset

CIS-BP Catalog of Inferred Sequence Binding Preferences

A freely available online database of transcription factor (TF) inferred…

A freely available online database of transcription factor (TF) inferred binding specificities. CIS-BP currently incorporates data from >300 species covering >250 TF families, totaling…

NGS-QC
Web

NGS-QC Next Generation Sequencing Quality Control generator

Evaluates the quality of ChIP-seq or enrichment-related Next Generation…

Evaluates the quality of ChIP-seq or enrichment-related Next Generation Sequencing (NGS) dataset relative to the datasets present in the entire database through our customized Galaxy platform…

GTRD
Dataset

GTRD Gene Transcription Regulation Database

Contains information on location in genome, structured information about cell…

Contains information on location in genome, structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. GTRD provides: (i)…

Factorbook
Dataset

Factorbook

A Wiki-based database for transcription factor-binding data generated by the…

A Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. In the first release, factorbook contains 457 ChIP-seq datasets on 119 TFs in a number of human cell…

DoOP
Dataset

DoOP Database of Orthologous Promoters

Stores eukaryotic promoter sequences. DoOP provides clusters of orthologous…

Stores eukaryotic promoter sequences. DoOP provides clusters of orthologous putative promoters within the phylum Chordata and kingdom Viridiplantae. The cluster sequences can be a source for a more…

ORegAnno
Dataset

ORegAnno Open REGulatory ANNOtation database

A resource for curated regulatory annotation. ORegAnno contains information…

A resource for curated regulatory annotation. ORegAnno contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other…

GenomeTrafac
Dataset

GenomeTrafac

Compiles information about conserved regulatory elements derived from…

Compiles information about conserved regulatory elements derived from orthologous sets of human and mouse genes analysis. GenomeTrafac contains the results of more than 12 000 RefSeq annotated human…

Popera
Desktop

Popera

A tool developed for DNase I hypersensitive sites (DHSs) identification. Popera…

A tool developed for DNase I hypersensitive sites (DHSs) identification. Popera identifies DHSs by applying the kernel density estimation algorithm. All the DHSs identified from various tissues and…

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SBR-Blood
Dataset

SBR-Blood hematopoietic Systems Biology Repository

Enables the user to conduct cell type correlations with previously published…

Enables the user to conduct cell type correlations with previously published data sets and data sets currently under investigation. By reproducing concepts manually validated in the community, it has…

PlantDHS
Dataset

PlantDHS

A plant DNase I hypersensitive site (DHS) database that integrates histone…

A plant DNase I hypersensitive site (DHS) database that integrates histone modification, RNA sequencing, nucleosome positioning/occupancy, transcription factor binding sites, and genomic sequence…

Pro54DB
Dataset

Pro54DB ?54 promoter database

A primary database of σ54 promoters and transcriptional regulation information…

A primary database of σ54 promoters and transcriptional regulation information curated from original scientific publications. In the current version, Pro54DB has stored 210 experimental-confirmed…

ABS
Dataset

ABS Annotated regulatory Binding Sites

A public database of known binding sites identified in promoters of orthologous…

A public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. ABS lists 650 experimental binding sites from 68…

Transcompel
Dataset

Transcompel

A database on composite elements. TRANSCompel focuses on so-called composite…

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…

BloodChIP
Dataset

BloodChIP

A user friendly database that integrates genome-wide binding profiles of…

A user friendly database that integrates genome-wide binding profiles of haematopoietic transcription factors in human blood cell types with chromatin accessibility profiles from the Human Epigenome…

ENCODE-motifs
Dataset

ENCODE-motifs

A database that uncovers the molecular basis of TF binding in the human genome…

A database that uncovers the molecular basis of TF binding in the human genome based on regulatory motif analysis of all Transcription Factors (TFs) grouped by family. This allows browsing of all…

TFBSshape
Dataset

TFBSshape

Provides DNA shape features for transcription factor binding sites (TFBSs) that…

Provides DNA shape features for transcription factor binding sites (TFBSs) that in addition to sequence features, usually in the form of position weight matrices (PWMs), characterize DNA binding…

CardioTF
Dataset

CardioTF

Captures all transcriptional information relating to cardiovascular…

Captures all transcriptional information relating to cardiovascular development. CardioTF is used to collate information on cardiovascular transcription factors (TFs), position weight matrices…

YY1TargetDB
Dataset

YY1TargetDB

Annotates and organizes YY1-binding loci and target motifs in a systematic way…

Annotates and organizes YY1-binding loci and target motifs in a systematic way with easy access. YY1TargetDB is a web-based relational database which collects YY1 binding loci from high-throughput…

FastBill
Desktop

FastBill

A software for prediction of evolutionarily conserved cis-regulatory modules.…

A software for prediction of evolutionarily conserved cis-regulatory modules. FastBill allows large-scale analyses, including multiple informant species. FastBill performs in a large-scale…

MycoRRdb
Dataset

MycoRRdb Mycobacterium Regulatory Region Database

Aims to identify the putative cis- regulatory sequences. MycoRRdb is a database…

Aims to identify the putative cis- regulatory sequences. MycoRRdb is a database that contains list of Reciprocal Best BLAST Hits (RBBHs) for more than 20 mycobacterial species. A search mode is…

DECRES
Desktop

DECRES DEep learning for identifying Cis-Regulatory ElementS

Based on the Deep Learning Tutorials and Theano. DECRES is developped for the…

Based on the Deep Learning Tutorials and Theano. DECRES is developped for the identification of CREs. This tool contains a supervised deep model – feedforward neural network (also known as…

AtRegNet
Web

AtRegNet Arabidopsis thaliana Regulatory Network

Documents and visualizes networks formed by transcription factors (TFs) and…

Documents and visualizes networks formed by transcription factors (TFs) and their direct target genes only. AtRegNet visualizes regulatory networks and allows quick access and download of any…

ChIP-Atlas
Dataset

ChIP-Atlas

A database with the result of analysis processed from the entire ChIP-Seq data…

A database with the result of analysis processed from the entire ChIP-Seq data archived in Sequence Read Archive (SRA). ChIP-Atlas is an integrative and comprehensive database for visualizing and…

CardioSignal
Dataset

CardioSignal

Provides online analysis tools to speeding up hypothesis-driven research in…

Provides online analysis tools to speeding up hypothesis-driven research in gene regulation. CardioSignal was designed for integration of regulatory information on the transcriptional regulation…

jaspextract
Desktop

jaspextract

Extract data from JASPAR. jaspextract accepts as input part of the uncompressed…

Extract data from JASPAR. jaspextract accepts as input part of the uncompressed and extracted Archive.zip file provided by JASPAR. JASPAR is a collection of transcription factor DNA-binding…

TransfactomeDB
Dataset

TransfactomeDB

A repository of sequence specificity models and condition-specific regulatory…

A repository of sequence specificity models and condition-specific regulatory activities for a large number of DNA- and RNA-binding proteins in Saccharomyces cerevisiae. The web interface allows the…

PreDREM
Dataset

PreDREM a database of Predicted DNA REgulatory Motifs in 349 human tissues and cells

A database of DNA regulatory motifs and motifs modules predicted from DNase I…

A database of DNA regulatory motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples. It contains 845-1325 predicted motifs in each sample, which…

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