Tag: epigenomics

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. G ...

The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular dia ...

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 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 ...

The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps through the characterization of the regulome, methylome, and transcriptome from a wide range of tissues and cell types. The IHEC Data Portal pr ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

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.

This resource details DNA methylation profiles in human and mouse brain. This database includes genome-wide DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end ...

EpiFactors is a web-accessible database that provides broad information about human proteins and complexes involved in epigenetic regulation. It also lists corresponding genes and their expression levels in several samples, in particular 458 human pr ...

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) ...

DNAmod is an open-source database (https://dnamod.hoffmanlab.org) that catalogues DNA modifications and provides a single source to learn about their properties. The database annotates the chemical properties and structures of all curated modified DN ...

4DGenome is a public database that archives and disseminates chromatin interaction data. Currently, 4DGenome contains over 8,038,248 interactions curated from both experimental studies (high throughput and individual studies) and computational predic ...

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 ...

DriverDB, a database that incorporates >9500 cancer-related RNA-seq datasets and >7000 more exome-seq datasets, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. Seven additi ...

>>>!!! <<< The Epigenomics database was retired on June 1, 2016. All epigenomics data are available in our GEO resource https://www.ncbi.nlm.nih.gov/geo >>> !!! <<< The Epigenomics database provides genomics maps of stable and reprogrammable nucl ...

Aging related omics data

HMM-based Identification of TF Footprints

Japanese Multi Omics Reference Panel

Epigenetic alterations, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and nucleosome positioning (NP), in cell-free DNA (cfDNA) have been widely observed in human diseases, and many available cfDNA-based epigenome-wide profiles exh ...

A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states a ...

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.

Arabidopsis thaliana Multi-omics Association Database

Brainbase is a data management, collaboration and sharing platform for the human neuroscience community. The platform provides private research collaboration workspaces, tools to flexibly organize and track subjects and sessions within studies, valid ...

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 major update of the ruminant functional and evolutionary genomics database.

VannoPortal is a variant annotation database that comprehensively collects and integrates genome-wide variant annotations and prediction scores from various biological domains, including allele frequency, linkage disequilibrium, evolutionary signatur ...

a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progressi ...

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

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 ...

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 ...

The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cy ...

A reference methylome database for different organisms that is created from public BS-seq datasets.

Sexual-dimorphism in human immune system ageing.

A database of extrachromosomal circular DNA profiles in human cancers.

Human microbiome affect the host epigenome.

A comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.

A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.

Database of circadian and ultradian transcripts in control tissues of kingdom-wide species.

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 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 ...

EpiMOLAS (Epi-genoMics OnLine Analysis System) is an intuitive web-based framework for genome-wide DNA methylation analysis.

Provide gene and epigenetics expression data useful for dissecting quantitative trait data in livestock. Future work will providedata tracks for these information sources and will ID tissue specific regulation information that is helpful in dissectin ...

Long-read-tools is an interactive database of software tools for the analysis of long read sequencing data.

A data hub for long genes. Long genes harbor specific genomic and epigenomic features and have been implicated in many human diseases. LongGeneDB is an interactive, visual database containing genomic information of 992 long genes (>200 kb) in 15 spe ...

An online tool for designing highly efficient sgRNAs targeting cell surface proteins

Data portal for standardized stem cell information. ICSCB is operated by CiRA,Kyoto University. It is an Intergerated Collection of Stem Cell Bank data by miacarm, standard data format for all the stem cell lines with minimum necessary information f ...

ChIP-Atlas is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape.

Provides a central data access hub for large collections of epigenomic data. It organizes the data from different sources using controlled vocabularies and ontologies. The data is stored in our server, where the users can access the data programmatic ...

The Open Archive for Miscellaneous Data (OMIX) database is a data repository developed and maintained by the National Genomics Data Center (NGDC). The database specializes in descriptions of biological studies, including genomic, proteomic, and metab ...

a comprehensive and interactive database of the silkworm | Silkworm Genome Informatics Database | e.g. FIBH or KWMTBOMO15365 or BGIBMGA005111 or silk fibroin heavy chain &nbspBrowse in Gene Lists | Search by sequence alignment against genomes or gene ...

TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios ...

>>>!!!<<< OMICtools is no longer online >>>!!!<<< We founded OMICtools in 2012 with the vision to drive progress in life science. We wanted to empower life science practitioners all over the world to achieve breakthroughs by getting data to talk. W ...