PceRBase: a database of plant competing endogenous RNA
Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Yuan, C., Meng, X., Li, X., Illing, N., Ingle, R. A., Wang, J., Chen, M. Tags: Database Issue Source Type: research
EURISCO: The European search catalogue for plant genetic resources
The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about 1.8 million crop plant accessions preserved by almost 400 institutes in Europe and beyond. EURISCO is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources. It is based on a network of National Inventories of 43 member countries and represents an important effort for the preservation of world's agrobiological diversity by providing information about the large genetic diversity kept by the collaborating collections. Moreover, EURISCO also assists its member countries in fulfilling legal oblig...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Weise, S., Oppermann, M., Maggioni, L., van Hintum, T., Knüpffer, H. Tags: Database Issue Source Type: research
Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors
Exposome-Explorer (http://exposome-explorer.iarc.fr) is the first database dedicated to biomarkers of exposure to environmental risk factors. It contains detailed information on the nature of biomarkers, their concentrations in various human biospecimens, the study population where measured and the analytical techniques used for measurement. It also contains correlations with external exposure measurements and data on biological reproducibility over time. The data in Exposome-Explorer was manually collected from peer-reviewed publications and organized to make it easily accessible through a web interface for in-depth analy...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Neveu, V., Moussy, A., Rouaix, H., Wedekind, R., Pon, A., Knox, C., Wishart, D. S., Scalbert, A. Tags: Database Issue Source Type: research
The Comparative Toxicogenomics Database: update 2017
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between chemicals and gene products, and their relationships to diseases. Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate expanded networks and predict novel associations. Today, core CTD includes more than 30.5 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, Gene Ontology (GO) annotations, pathways, and gene interaction mo...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., King, B. L., McMorran, R., Wiegers, J., Wiegers, T. C., Mattingly, C. J. Tags: Database Issue Source Type: research
CEBS: a comprehensive annotated database of toxicological data
The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to relea...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Lea, I. A., Gong, H., Paleja, A., Rashid, A., Fostel, J. Tags: Database Issue Source Type: research
PubChem BioAssay: 2017 update
PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databas...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Wang, Y., Bryant, S. H., Cheng, T., Wang, J., Gindulyte, A., Shoemaker, B. A., Thiessen, P. A., He, S., Zhang, J. Tags: Database Issue Source Type: research
The ChEMBL database in 2017
ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 and 2014 Nucleic Acids Research Database Issues. Since then, alongside the continued extraction of data from the medicinal chemistry literature, new sources of bioactivity data have also been added to the database. These include: deposited data sets from neglected disease screening; crop protection data; drug metabolism and disposition data and bioactivity data from patents. A number of improvements and new features have also been incorporated. These include the annotation of assays and targets using ontologi...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Gaulton, A., Hersey, A., Nowotka, M., Bento, A. P., Chambers, J., Mendez, D., Mutowo, P., Atkinson, F., Bellis, L. J., Cibrian-Uhalte, E., Davies, M., Dedman, N., Karlsson, A., Magarinos, M. P., Overington, J. P., Papadatos, G., Smit, I., Leach, A. R. Tags: Database Issue Source Type: research
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines
OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbat...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Chen, W.-H., Lu, G., Chen, X., Zhao, X.-M., Bork, P. Tags: Database Issue Source Type: research
DrugCentral: online drug compendium
DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to externa...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Ursu, O., Holmes, J., Knockel, J., Bologa, C. G., Yang, J. J., Mathias, S. L., Nelson, S. J., Oprea, T. I. Tags: Database Issue Source Type: research
YM500v3: a database for small RNA sequencing in human cancer research
We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-se...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Chung, I.-F., Chang, S.-J., Chen, C.-Y., Liu, S.-H., Li, C.-Y., Chan, C.-H., Shih, C.-C., Cheng, W.-C. Tags: Database Issue Source Type: research
SZGR 2.0: a one-stop shop of schizophrenia candidate genes
SZGR 2.0 is a comprehensive resource of candidate variants and genes for schizophrenia, covering genetic, epigenetic, transcriptomic, translational and many other types of evidence. By systematic review and curation of multiple lines of evidence, we included almost all variants and genes that have ever been reported to be associated with schizophrenia. In particular, we collected ~4200 common variants reported in genome-wide association studies, ~1000 de novo mutations discovered by large-scale sequencing of family samples, 215 genes spanning rare and replication copy number variations, 99 genes overlapping with linkage re...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Jia, P., Han, G., Zhao, J., Lu, P., Zhao, Z. Tags: Database Issue Source Type: research
KERIS: kaleidoscope of gene responses to inflammation between species
A cornerstone of modern biomedical research is the use of animal models to study disease mechanisms and to develop new therapeutic approaches. In order to help the research community to better explore the similarities and differences of genomic response between human inflammatory diseases and murine models, we developed KERIS: kaleidoscope of gene responses to inflammation between species (available at http://www.igenomed.org/keris/). As of June 2016, KERIS includes comparisons of the genomic response of six human inflammatory diseases (burns, trauma, infection, sepsis, endotoxin and acute respiratory distress syndrome) an...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Li, P., Tompkins, R. G., Xiao, W., the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program Tags: Database Issue Source Type: research
NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases
The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs. Mining and summarizing NSD–ncRNA asso...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Wang, J., Cao, Y., Zhang, H., Wang, T., Tian, Q., Lu, X., Lu, X., Kong, X., Liu, Z., Wang, N., Zhang, S., Ma, H., Ning, S., Wang, L. Tags: Database Issue Source Type: research
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: MacArthur, J., Bowler, E., Cerezo, M., Gil, L., Hall, P., Hastings, E., Junkins, H., McMahon, A., Milano, A., Morales, J., Pendlington, Z. M., Welter, D., Burdett, T., Hindorff, L., Flicek, P., Cunningham, F., Parkinson, H. Tags: Database Issue Source Type: research
DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database
The human disease methylation database (DiseaseMeth, http://bioinfo.hrbmu.edu.cn/diseasemeth/) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease–gene associations from 216 201 to 679 602. ...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Xiong, Y., Wei, Y., Gu, Y., Zhang, S., Lyu, J., Zhang, B., Chen, C., Zhu, J., Wang, Y., Liu, H., Zhang, Y. Tags: Database Issue Source Type: research
