Tag: epigenetics

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 ...

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

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 ...

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 ...

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 ...

HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.

The human disease methylation database, DiseaseMeth is a web based resource focused on the aberrant methylomes of human diseases. Until recently, bulks of large-scale data are avaible and are increasingly grown, from which more information can be min ...

DNMIVD is a comprehensive annotation and interactive visualization database for DNA methylation profile of diverse human cancer constructed with high throughput microarray data from TCGA and GEO databases, and it also integrates some data from Pancan ...

piRBase stores information on piRNAs and piRNA-associated data to support piRNA functional analysis.

Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.

Genomic Expression Archive (GEA) is a public database of functional genomics data such as gene expression, epigenetics and genotyping SNP array. Both microarray- and sequence-based data are accepted in the MAGE-TAB format in compliance with MIAME and ...

Human Histone Modification Database

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

>>>!!! <<< 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 ...

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets bro ...

Database of Human Lung Cancer Research

Autosomal monoallelic expression (MAE) refers to mitotically stable, epigenetically controlled allele-specific expression of autosomal genes, with the initial non-predetermined ('random') choice of thetranscriptional activity of the two alleles maint ...

A manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple specie ...

The database contains information about the occurrence of methylated cytosines in the DNA.

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 ...

A database for systems biology of DNA dynamics during the cell life.

A database of curated mutual regulation between miRNAs and epigenetic modifications.

PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation. PhenoModifier provides a more complete spectrum of genetic factors contributing to human phenotypic variation and the portal has a broad sci ...

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, ...

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 ...

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides ...

Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide ...

A comprehensive database established to offer a web-based access to founder mutation data in Mediterranean population. The database provides an overview about the spectrum of founder mutations found in Mediterranean population to the scientific commu ...

CRISPR/Cas9 Off-Target Cleavage Assays

Human Assay-for-Transposase-Accessible Chromatin data

A database of epigenome-wide association studies.

Making Omics Data Useful to the Broader Scientific Community. Metabolic Disorders Knowledge Portal. ||| CORRECT NAME OF TOOL COULD ALSO BE 'MSK-KP'

CHG is a systematically integrated database of cancer hallmark genes. The database focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes.

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 ...

ConsRM is a collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome.

Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data | CancerDAP is a database molecularly characterizing subpathways involved in cellular response to 191 anticancer drugs | 1 Prospect the deta ...

The structural genomics of histone tail recognition web server is an open access resource that presents within mini articles all publicly available experimental structures of histone tails in complex with human proteins. Each article is composed of i ...

Variants of DNA mismatch repair genes derived from 33,998 Chinese individuals with and without cancer reveal their highly ethnic-specific nature. An open-access database of DNA mismatch repair (MMR) gene variants in Chinese population. DNA mismatch ...

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

Autophagy and Tumor Database (ATdb) is a database used to compile the published information concerning autophagy and tumor research. Such a database can be used for optaining an in-depth understanding of the complex correlations between autophagy and ...

TwinsUK follows the lives of adult twins to understand how genetic variation relates to health and ageing. Over 30 years, collected data comprises self-reported, physical and cognitive measures, biochemical measures, 'omics and a wealth of biosamples ...

An interactive online database for analysis of gene expression and viral infection in cancer.

Fusion gene annotation updates aided by deep learning.

AddictGene is an integrated knowledge base for differentially expressed genes associated with psychostimulants,

A database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses.

ADEx: Autoimmune Diseases Explorer is a comprehensive and centralized database for exploring omics data in Autoimmune Diseases. The database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most ...

The EPIC Norfolk study is a population-based prospective cohort study. EPIC-Norfolk is part of the European Prospective Investigation of Cancer (EPIC), a large multi-centre cohort study with participants enrolled from 23 centres across Europe

GUIdEStaR (G-quadruplex, uORF, IRES, Epigenetics, Small RNA, Repeats) is the integrated metadatabase in conjunction with neural network methods.

Database of human genotype-phenotype associations.

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

Haloarchaeal genomes database.

Comparative transcriptomics and co-expression database for bacterial pathogens.

A comprehensive enrichment analysis software for human genomic regions.

Sepsis single-cell whole gene expression database.

Multi-omics molecular biomarkers and database of osteoarthritis.

A manually curated database for the differential methylation in Alzheimer's disease.

An integrated database for sex differences in cancer.

An integrated transcriptomic and genomic database for Bombyx mori and related species.

An integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.

A database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.

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

ADVP is a platform for the public community to browse, search and understand Alzheimer's Disease genetics findings easily. .

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

BCGene is a online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer

a comprehensive genetic database of Parkinson's disease. Gene4PD: an integrative genomic database and analytic platform for Parkinson's disease. Rare variants identified from PD patients.

Buffalo Subclinical Mastitis Methylome–Transcriptome database (BSCM2TDb) is a three-tier architecture-based relational database in Water Buffalo.

FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase) is a comprehensive cell-free DNA (cfDNA) fragmentation pattern database to host uniformly processed and quality controlled paired-end cfDNA WGS datasets.

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 ...

Allele-Specific DNA Methylation Databases (ASMdb) is a comprehensive database for allele-specific DNA methylation in diverse organisms. ASMdb is aiming to provide a comprehensive resource and a web tool for showing the DNA methylation level and diffe ...

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

The Chinese Glioma Genome Atlas (CGGA) is a user-friendly web application for data storage and analysis to explore brain tumors datasets. This database includes the whole-exome sequencing, DNA methylation, mRNA sequencing, mRNA microarray and microRN ...

BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analy ...

A comprehensive genetic resource of nicotine and smoking. Genetic resources of nicotine and smoking. Genetic Resources Of Nicotine and Smoking (GRONS) is a database devoted to provide a comprehensive and systematic collection of cross-platform gene ...

A database for exploring N6-methyladenosine methylome. REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications. Curre ...

The Male Fertility Gene Atlas – A web tool for collecting and integrating data about epi-/genetic causes of male infertility. The Male Fertility Gene Atlas (MFGA) is a public platform for providing a fast, simple and straightforward access to OMICS ...

A data-driven social network connecting scientists to genomics datasets. ORSO (Online Resource for Social Omics) is a web application designed to help users find next generation sequencing (NGS) datasets relevant to their research interests. ORSO per ...