Table 3.
Large-scale epigenome projects.
| PROJECTS AND WEBSITES | SUMMARY |
|---|---|
| IHEC (International Human Epigenome Consortium) (http://ihec-epigenomes.org) | IHEC launched with a goal to understand to what extent the epigenome has shaped the human population genetically and in response to the environment by coordinating the reference maps of human epigenomes for key cellular states in health and diseases status. It has been distributed to multiple contributing projects including the NIH Roadmap, the ENCODE and the BLUEPRINT projects. |
| NIH Roadmap Epigenomics Mapping Consortium (http://www.roadmapepigenomics.org/) | The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The Consortium expects to deliver a collection of normal epigenomes that will provide a framework or reference for comparison and integration within a broad array of future studies. |
| ENCODE (Encyclopedia of DNA Elements) (https://www.encodeproject.org/) | The ENCODE 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 in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. Although epigenome mapping is not its main goal, the project includes largescale mapping of DNA methylation, histone modifications and other epigenetic information. |
| BLUEPRINT (http://www.blueprint-epigenome.eu/) | BLUEPRINT is a large-scale research project receiving close to 30 million euro funding from the EU. 39 leading European universities, research institutes and industry entrepreneurs participate in what is one of the two first so-called high impact research initiatives to receive funding from the EU. |
| HEP (Human Epigenome Project) (http://www.epigenome.org/) | The partially EU-funded HEP analyzed DNA methylation in 43 unrelated individuals at single basepair resolution. Although the analysis was confined to selected regions on three chromosomes, it is the largest high-resolution, multiindividual epigenome dataset published to date. |
| German DEEP project (http://www.deutsches-epigenom-programm.de/) | DEEP focuses on the analysis of cells connected to complex diseases with high socio-economic impact: metabolic diseases such as steatosis and adipositas as well as inflammatory diseases of the joints and the intestine. DEEPs goal is to generate high-end data for comprehensive biomedical interpretation of healthy and diseased cells. With this DEEP will contribute to discover new functional epigenetic links useful for clinical diagnosis, therapy and health risk prevention. All data generated will be made publically available and will be integrated into a sustainable world-wide data structure comprised by the IHEC initiative. |
| HEROIC (High-throughput Epigenetic Regulatory Organisation In Chromatin) (EU) (http://projects.ensembl.org/heroic/) | The HEROIC project is a multi-center EU project that applies ChIP-on-chip, chromosome interaction analysis and whole-genome nuclear localization assays to understanding human genome regulation. |
| AHEAD (Alliance for Human Epigenomics and Disease) Task Force (international) (http://graphy21.blogspot.com) | The goal of the AHEAD is to initiate and coordinate a comprehensive human epigenome-mapping project. Initially, focus is set on developing a suitable bioinformatic infrastructure and on performing epigenome mapping in a selection of normal tissues, which may provide the reference for subsequent mapping in abnormal cells. |
| ICGC (International Cancer Genome Consortium) (https://icgc.org/) | The goal of the ICGC is to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe. |
| TCGA (The Cancer Genome Atlas) (http://cancergenome.nih.gov) | The Cancer Genome Atlas (TCGA), collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), aims to generate comprehensive, multi-dimensional maps of the key genomic changes in major types and subtypes of cancer. |
| FANTOM project (http://fantom.gsc.riken.jp/) | FANTOM is an international research consortium established to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN. FANTOM developed and expanded over time to encompass the fields of transcriptome analysis. FANTOM database and the FANTOM full-length cDNA clone bank are worldwide available resources that already fueled the iPS development. |
| GENECODE project (https://www.gencodegenes.org/) | GENCODE as a sub-project of the ENCODE scale-up project are aiming to integrated annotation of gene features. Currently running phase is continuously to improve the coverage and accuracy of the human and mouse gene set by enhancing and extending the annotation of all evidence-based gene features at a high accuracy, including protein-coding loci with alternatively splices variants, non-coding loci and pseudogenes. |
Note: *The descriptions are adapted from indicated website sources.