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http://www.bioinformatics.org/peakanalyzer/wiki/

A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

Proper citation: PeakAnalyzer (RRID:SCR_001194) Copy   

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http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

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http://www.creline.org/

The CREATE consortium represents a core of major European and international mouse database holders and research groups involved in conditional mutagenesis, primarily to develop a strategy for the integration and dissemination of Cre driver strains for modelling aspects of complex human diseases in the mouse. Collectively the participants have amassed a significant number of these strains in their respective databases. Therefore one of the goals of CREATE is to provide a unified portal for worldwide access to these critical resources. The portal can either be searched through an advanced BioMart interface, by driver name, or by anatomical site of expression using Embryonic Mouse Anatomy Project (EMAP) and Mouse Anatomy (MA) ontology terms. Search results link back to the original source of the data for more detailed information and to IMSR to order mice if available. The ontology browser is particularly useful as it enables the CREATE consortium to identify cell and tissues that are not currently covered by existing lines. CREATE also aims to coordinate the production of suitable lines by the Cre generation projects described above. Through the CREATE portal, the CREATE consortium aims to develop a strategy for the production, integration and dissemination of new Cre driver strains for modelling aspects of complex human diseases in the mouse. CREATE is also developing a roadmap for harnessing emerging technologies and methods for improving Cre-mediated recombination in vivo through targeted, intensive workshops and discussion forums on the portal. This will entail review of construct design options for classical transgenic constructs (promoter/enhancer used, small size <2025 Kb) vs large transgenic constructs (BAC, P1, YAC etc.); methods used for Cre transgenic lines including random vs targeted integration, position independent expression loci, or replacement of endogenous coding sequences with Cre recombinase under the control of the endogenous locus. CREATE provides a platform for discussion of additional issues specific to inducible Cre strategies including background activity before induction, inducibility (kinetics), efficiency, and protocols used for induction of Cre recombinase activity. Additional components of the technology roadmap will be the cataloguing of other existing methodologies (rtTA, FLP, Dre) of mouse genome modification, sharing information on validated Cre mutant lines as well as identification and assessment of new methods of mutagenesis such as RNAi and other emerging technologies. Other discussion topics addressed through surveys on the CREATE portal include the characterization of Cre lines (specificity of expression/deletion; efficiency of expression/ deletion; reproducibility of deletion from animal to animal for the same floxed allele; reproducibility with different floxed alleles; timing of expression/deletion, etc.), the extent to which Cre expression changes upon backcrossing to specific genetic backgrounds through variegation and silencing; potential phenotypes caused by either integration- mediated mutagenesis or Cre ''toxicity''; and other factors affecting the specificity of Cre-mediated expression/deletion. CREATE regularly integrates common fields from the Cre-X, CreZOO and the MGI recombinase portal resources described below. The data in common consists of: * Transgene or Knock-in name. * MGI ID of allele. * Driver. * Anatomical site of expression. * Pubmed ID. * IMSR strain name and link. * Inducibility (YES/NO).

Proper citation: CREATE (RRID:SCR_006133) Copy   

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http://www.blueprint-epigenome.eu/

Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. At EBI, the ftp site with the data can be found. You can either opt to link to the track hubs yourself or you can add the track hub to a genome browser - UCSC or ENSEMBL. Also Meta Data files and README are available. The data can also be accessed via the BIOMART system.

Proper citation: Blueprint Epigenome (RRID:SCR_003844) Copy   

•   Source: SciCrunch Registry
  

http://www.reactome.org

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

Proper citation: Reactome (RRID:SCR_003485) Copy   

•   Source: SciCrunch Registry
  

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

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http://www.ncbi.nlm.nih.gov/CCDS/

Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly.

Proper citation: Consensus CDS (RRID:SCR_006729) Copy   

•   Source: SciCrunch Registry