MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search
The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ~20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symptoms, Anatomical Context, Drugs, Genetic Tests, Variations and Publications. The Aliases and Classifications section reflects an algorithm for disease name integration across often-conflicting sources, providing effective annotation consolidation. A central feature is a balanced Genes section, with scores refl...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Rappaport, N., Twik, M., Plaschkes, I., Nudel, R., Iny Stein, T., Levitt, J., Gershoni, M., Morrey, C. P., Safran, M., Lancet, D. Tags: Database Issue Source Type: research
IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex
The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resou...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Maccari, G., Robinson, J., Ballingall, K., Guethlein, L. A., Grimholt, U., Kaufman, J., Ho, C.-S., de Groot, N. G., Flicek, P., Bontrop, R. E., Hammond, J. A., Marsh, S. G. E. Tags: Database Issue Source Type: research
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data
The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Clarke, L., Fairley, S., Zheng-Bradley, X., Streeter, I., Perry, E., Lowy, E., Tasse, A.-M., Flicek, P. Tags: Database Issue Source Type: research
Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies
FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Viennas, E., Komianou, A., Mizzi, C., Stojiljkovic, M., Mitropoulou, C., Muilu, J., Vihinen, M., Grypioti, P., Papadaki, S., Pavlidis, C., Zukic, B., Katsila, T., van der Spek, P. J., Pavlovic, S., Tzimas, G., Patrinos, G. P. Tags: Database Issue Source Type: research
The ExAC browser: displaying reference data information from over 60 000 exomes
Worldwide, hundreds of thousands of humans have had their genomes or exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for exome sequence data from 60 706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Karczewski, K. J., Weisburd, B., Thomas, B., Solomonson, M., Ruderfer, D. M., Kavanagh, D., Hamamsy, T., Lek, M., Samocha, K. E., Cummings, B. B., Birnbaum, D., The Exome Aggregation Consortium, Daly, M. J., MacArthur, D. G. Tags: Database Issue Source Type: research
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Pinero, J., Bravo, A., Queralt-Rosinach, N., Gutierrez-Sacristan, A., Deu-Pons, J., Centeno, E., Garcia-Garcia, J., Sanz, F., Furlong, L. I. Tags: Database Issue Source Type: research
dbSAP: single amino-acid polymorphism database for protein variation detection
Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in amino-acid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments. Here, we present the dbSAP database for conveniently accessing the comprehensive...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Cao, R., Shi, Y., Chen, S., Ma, Y., Chen, J., Yang, J., Chen, G., Shi, T. Tags: Database Issue Source Type: research
The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data
The database of Genotypes and Phenotypes (dbGaP) Data Browser (https://www.ncbi.nlm.nih.gov/gap/ddb/) was developed in response to requests from the scientific community for a resource that enable view-only access to summary-level information and individual-level genotype and sequence data associated with phenotypic features maintained in the controlled-access tier of dbGaP. Until now, the dbGaP controlled-access environment required investigators to submit a data access request, wait for Data Access Committee review, download each data set and locally examine them for potentially relevant information. Existing unrestricte...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Wong, K. M., Langlais, K., Tobias, G. S., Fletcher-Hoppe, C., Krasnewich, D., Leeds, H. S., Rodriguez, L. L., Godynskiy, G., Schneider, V. A., Ramos, E. M., Sherry, S. T. Tags: Database Issue Source Type: research
dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers
MicroRNAs (miRNAs) are often deregulated in cancer and are thought to play an important role in cancer development. Large amount of differentially expressed miRNAs have been identified in various cancers by using high-throughput methods. It is therefore quite important to make a comprehensive collection of these miRNAs and to decipher their roles in oncogenesis and tumor progression. In 2010, we presented the first release of dbDEMC, representing a database for collection of differentially expressed miRNAs in human cancers obtained from microarray data. Here we describe an update of the database. dbDEMC 2.0 documents 209 e...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Yang, Z., Wu, L., Wang, A., Tang, W., Zhao, Y., Zhao, H., Teschendorff, A. E. Tags: Database Issue Source Type: research
denovo-db: a compendium of human de novo variants
Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (http://denovo-db.gs.washington.edu), a database for human de novo variants. As of ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Turner, T. N., Yi, Q., Krumm, N., Huddleston, J., Hoekzema, K., F. Stessman, H. A., Doebley, A.-L., Bernier, R. A., Nickerson, D. A., Eichler, E. E. Tags: Database Issue Source Type: research
mirDNMR: a gene-centered database of background de novo mutation rates in human
In conclusion, mirDNMR (https://www.wzgenomics.cn/mirdnmr/) can be widely used to identify the genetic basis of sporadic genetic diseases. (Source: Nucleic Acids Research)
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Jiang, Y., Li, Z., Liu, Z., Chen, D., Wu, W., Du, Y., Ji, L., Jin, Z.-B., Li, W., Wu, J. Tags: Database Issue Source Type: research
ChiTaRS-3.1--the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions
Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922 chimeric transcripts along with 11 714 cancer breakpoints. In this latest version, we have included multiple cross-references to GeneCards, iHop, PubMed, NCBI, Ensembl, OMIM, ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Gorohovski, A., Tagore, S., Palande, V., Malka, A., Raviv-Shay, D., Frenkel-Morgenstern, M. Tags: Database Issue Source Type: research
ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining
Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Lee, M., Lee, K., Yu, N., Jang, I., Choi, I., Kim, P., Jang, Y. E., Kim, B., Kim, S., Lee, B., Kang, J., Lee, S. Tags: Database Issue Source Type: research
COSMIC: somatic cancer genetics at high-resolution
COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Mol...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Forbes, S. A., Beare, D., Boutselakis, H., Bamford, S., Bindal, N., Tate, J., Cole, C. G., Ward, S., Dawson, E., Ponting, L., Stefancsik, R., Harsha, B., Kok, C. Y., Jia, M., Jubb, H., Sondka, Z., Thompson, S., De, T., Campbell, P. J. Tags: Database Issue Source Type: research
AAgAtlas 1.0: a human autoantigen database
Autoantibodies refer to antibodies that target self-antigens, which can play pivotal roles in maintaining homeostasis, distinguishing normal from tumor tissue and trigger autoimmune diseases. In the last three decades, tremendous efforts have been devoted to elucidate the generation, evolution and functions of autoantibodies, as well as their target autoantigens. However, reports of these countless previously identified autoantigens are randomly dispersed in the literature. Here, we constructed an AAgAtlas database 1.0 using text-mining and manual curation. We extracted 45 830 autoantigen-related abstracts and 94 313 sente...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Wang, D., Yang, L., Zhang, P., LaBaer, J., Hermjakob, H., Li, D., Yu, X. Tags: Database Issue Source Type: research
