The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model or...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Howe, D. G., Bradford, Y. M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S. T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. Tags: Database Issue Source Type: research
REDIportal: a comprehensive database of A-to-I RNA editing events in humans
RNA editing by A-to-I deamination is the prominent co-/post-transcriptional modification in humans. It is carried out by ADAR enzymes and contributes to both transcriptomic and proteomic expansion. RNA editing has pivotal cellular effects and its deregulation has been linked to a variety of human disorders including neurological and neurodegenerative diseases and cancer. Despite its biological relevance, many physiological and functional aspects of RNA editing are yet elusive. Here, we present REDIportal, available online at http://srv00.recas.ba.infn.it/atlas/, the largest and comprehensive collection of RNA editing in hu...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Picardi, E., D'Erchia, A. M., Lo Giudice, C., Pesole, G. Tags: Database Issue Source Type: research
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Zdobnov, E. M., Tegenfeldt, F., Kuznetsov, D., Waterhouse, R. M., Simao, F. A., Ioannidis, P., Seppey, M., Loetscher, A., Kriventseva, E. V. Tags: Database Issue Source Type: research
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse
The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associations of those features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases. MGD continues to enhance access to these data, to extend the scope of data content and visualizations, and to provide infrastructure and user support that ensures effective and eff...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Blake, J. A., Eppig, J. T., Kadin, J. A., Richardson, J. E., Smith, C. L., Bult, C. J., the Mouse Genome Database Group Tags: Database Issue Source Type: research
New data and features for advanced data mining in Manteia
Manteia is an integrative database available online at http://manteia.igbmc.fr which provides a large array of OMICs data related to the development of the mouse, chicken, zebrafish and human. The system is designed to use different types of data together in order to perform advanced datamining, test hypotheses or provide candidate genes involved in biological processes or responsible for human diseases. In this new version of the database, Manteia has been enhanced with new expression data originating from microarray and next generation sequencing experiments. In addition, the system includes new statistics tools to analy...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Tassy, O. Tags: Database Issue Source Type: research
HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here descri...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Clima, R., Preste, R., Calabrese, C., Diroma, M. A., Santorsola, M., Scioscia, G., Simone, D., Shen, L., Gasparre, G., Attimonelli, M. Tags: Database Issue Source Type: research
The human-induced pluripotent stem cell initiative--data resources for cellular genetics
The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Streeter, I., Harrison, P. W., Faulconbridge, A., The HipSci Consortium, Flicek, P., Parkinson, H., Clarke, L. Tags: Database Issue Source Type: research
HieranoiDB: a database of orthologs inferred by Hieranoid
HieranoiDB (http://hieranoiDB.sbc.su.se) is a freely available on-line database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. It infers orthologs at each node in a species guide tree with the InParanoid algorithm as it progresses from the leaves to the root. Here we present a database HieranoiDB with a web interface that makes it easy to search and visualize the output of Hieranoid, and to download it in various formats. Searching can be performed using protein description, identifier or sequence. In this first version, orthologs are available for the 66 Quest for Orthologs reference proteomes. ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kaduk, M., Riegler, C., Lemp, O., Sonnhammer, E. L. L. Tags: Database Issue Source Type: research
GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens
Over the past years, CRISPR/Cas9 mediated genome editing has developed into a powerful tool for modifying genomes in various organisms. In high-throughput screens, CRISPR/Cas9 mediated gene perturbations can be used for the systematic functional analysis of whole genomes. Discoveries from such screens provide a wealth of knowledge about gene to phenotype relationships in various biological model systems. However, a database resource to query results efficiently has been lacking. To this end, we developed GenomeCRISPR (http://genomecrispr.org), a database for genome-scale CRISPR/Cas9 screens. Currently, GenomeCRISPR contain...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Rauscher, B., Heigwer, F., Breinig, M., Winter, J., Boutros, M. Tags: Database Issue Source Type: research
FlyRNAi.org--the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update
The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation. In this update, we describe recent changes and additions ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Hu, Y., Comjean, A., Roesel, C., Vinayagam, A., Flockhart, I., Zirin, J., Perkins, L., Perrimon, N., Mohr, S. E. Tags: Database Issue Source Type: research
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse
Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin acc...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Mei, S., Qin, Q., Wu, Q., Sun, H., Zheng, R., Zang, C., Zhu, M., Wu, J., Shi, X., Taing, L., Liu, T., Brown, M., Meyer, C. A., Liu, X. S. Tags: Database Issue Source Type: research
CeNDR, the Caenorhabditis elegans natural diversity resource
Studies in model organisms have yielded considerable insights into the etiology of disease and our understanding of evolutionary processes. Caenorhabditis elegans is among the most powerful model organisms used to understand biology. However, C. elegans is not used as extensively as other model organisms to investigate how natural variation shapes traits, especially through the use of genome-wide association (GWA) analyses. Here, we introduce a new platform, the C. elegans Natural Diversity Resource (CeNDR) to enable statistical genetics and genomics studies of C. elegans and to connect the results to human disease. CeNDR ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Cook, D. E., Zdraljevic, S., Roberts, J. P., Andersen, E. C. Tags: Database Issue Source Type: research
3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes
The vast noncoding portion of the human genome harbors a rich array of functional elements and disease-causing regulatory variants. Recent high-throughput chromosome conformation capture studies have outlined the principles of these elements interacting and regulating the expression of distal target genes through three-dimensional (3D) chromatin looping. Here we present 3DSNP, an integrated database for annotating human noncoding variants by exploring their roles in the distal interactions between genes and regulatory elements. 3DSNP integrates 3D chromatin interactions, local chromatin signatures in different cell types a...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Lu, Y., Quan, C., Chen, H., Bo, X., Zhang, C. Tags: Database Issue Source Type: research
Genenames.org: the HGNC and VGNC resources in 2017
The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. Currently the HGNC database contains almost 40 000 approved gene symbols, over 19 000 of which represent protein-coding genes. In addition to naming genomic loci we manually curate genes into family sets based on shared characteristics such as homology, function or phenotype. We have recently updated our gene family resources and introduced new improved visualizations which can be seen alongside our gene symbol reports on our primary website http://www.genenames.org. In 2016...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Yates, B., Braschi, B., Gray, K. A., Seal, R. L., Tweedie, S., Bruford, E. A. Tags: Database Issue Source Type: research
World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide
The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)—Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue info...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Wu, L., Sun, Q., Desmeth, P., Sugawara, H., Xu, Z., McCluskey, K., Smith, D., Alexander, V., Lima, N., Ohkuma, M., Robert, V., Zhou, Y., Li, J., Fan, G., Ingsriswang, S., Ozerskaya, S., Ma, J. Tags: Database Issue Source Type: research
