Database maintenance site: La Trobe Institute for Molecular Sciences
Organism(s) covered:All
Description: Vesiclepedia is a manually curated compendium of molecular data (lipid, RNA and protein) identified in Extracellular vesicles. The Extracellular vesicles are classified into fol...Show Details...
Database maintenance site: University of Melbourne
Organism(s) covered:Homo sapiens | Mus musculus
Description: Stemformatics is a web-based data platform to find interesting genes in gene expression datasets of stem cells. It contains public gene expression datasets derived from microarr...Show Details...
Description: OrthoInspector is a catalog of orthologs predicted across three domains of life, Eukaryota, Bacteria, and Archaea. Each entry provides a fully searchable list of orthologs and i...Show Details...
Description: MoonDB is a database of predicted and manually curated extreme multifunctional (EMF) proteins and moonlighting proteins, which are proteins that perform multiple unrelated funct...Show Details...
Database maintenance site: College of Bioinformatics Science and Technology, Harbin Medical University
Organism(s) covered:all
Description: LncACTdb is a database for LncRNA-Associated Competing Triplets (LncACT). It provides manually curated and predicted ceRNA interactions. The class of ceRNAs in LncACTdb contains...Show Details...
Database maintenance site: Network Biomedicine Lab, Yonsei University, Marcotte Lab, University of Texas at Austin
Organism(s) covered:Homo sapiens
Description: HumanNet is a database for human gene networks, which integrates diverse types of omics data and provides gene-disease associations by their own network inference algorithms. Us...Show Details...
Database maintenance site: The Walter and Eliza Hall Institute of Medical Research
Organism(s) covered:Homo sapiens | Mus musculus
Description: Haemosphere is a data portal for RNA-Seq datasets, including each celltype of the dataset, cell_lineage, tissue, treatment, immunophenotype, species, and strain, etc. It contain...Show Details...
Description: GENCODE is a database to identify and classify all gene features in the human and mouse genomes. It provides foundational reference genome annotation, and includes comprehensive...Show Details...
Database maintenance site: University of Washington
Organism(s) covered:Homo sapiens
Description: It is a site for Combined Annotation-Dependent Depletion (CADD), which is a framework for scoring the deleteriousness of single nucleotide variants as well as insertion/deletion...Show Details...
Database maintenance site: Weizmann Institute of Science
Organism(s) covered:Saccharomyces cerevisiae
Description: YeastRGB is a database for abundance and localization of proteins in Saccharomyces cerevisiae. It provides fluorescence microscopy data of yeasts, which were introduced ORF libr...Show Details...
Database maintenance site: LCSB (Luxembourg Centre for Systems Biomedicine of the University of Luxembourg)
Organism(s) covered:Homo sapiens | Bacteria
Description: VMH is an integrated database for human and gut microbial metabolisms linked to diseases and nutritional data. The core data are hundreds of genome-scale metabolic reconstructio...Show Details...
Description: Victors is a database about virulence factors (VFs) collected by manual curation from peer-reviewed publications. Those VFs come from pathogenic organisms showed pathogenicity t...Show Details...
Description: UniLectin is a database for manually curated and predicted lectins. It provides information about the classification and curation of lectins (with UniLectin3D module), the predi...Show Details...
Database maintenance site: RIKEN BRC (RIKEN BioResource Research Center)
Organism(s) covered:Mus musculus
Description: MoG+ is a mouse genome database which shows mouse genomic variation visually to compare inbred mouse strains established in Japan (JF1/Ms etc.) to frequently used classical inbr...Show Details...
Database maintenance site: RIKEN BRC (RIKEN BioResource Research Center)
Organism(s) covered:All
Description: BioResource MetaDatabase is a data repository for metadata of bioresources in RIKEN. This database provides life-science data in the bases of standardized metadata techniques in...Show Details...
Description: Trips-viz is a database for Ribosome profiling (Ribo-seq) data that have been produced using publicly available ribosome profiling and corresponding RNA-seq datasets from SRA.Tr...Show Details...
Database maintenance site: Beijing University of Chinese Medicine
Organism(s) covered:Homo sapiens
Description: SymMap is a database for integration with traditional Chinese medicine (TCM) and modern medicine (MM) through both internal molecular mechanism and external symptom mapping. It ...Show Details...
Database maintenance site: Agricultural Genetic Engineering Research Institute
Organism(s) covered:All
Description: SSRome is an integrated database and pipelines for exploring microsatellites in a wide range of organisms. It contains microsatellite DNA motifs which were identified across Pla...Show Details...
Database maintenance site: Harbin Medical University
Organism(s) covered:Homo sapiens
Description: SEdb is a database about super-enhancers in gene regulation. It collects detailed genetic and epigenetic annotation information on super-enhancers, including common SNPs, motif ...Show Details...
Description: RNAct is a database of the protein–RNA interactome. RNA-binding proteins (RBPs) are collected from experimental interaction data or predicted from SONAR and catRAPID (protein–RN...Show Details...
Database maintenance site: INRAE (National Research Institute for Agriculture, Food and Environment)
Organism(s) covered:All
Description: RetroRules is a database of reaction rules for metabolic pathway. It provides a complete set of reaction rules, which were extracted from public databases and expressed in the c...Show Details...
Database maintenance site: Sun Yat-sen University Cancer Center
Organism(s) covered:Homo sapiens
Description: qPhos is a database for comprehensive resource of protein phosphorylation in human tissues and cell lines. The data were curated from published literatures to provide protein ph...Show Details...
Database maintenance site: Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona
Organism(s) covered:Homo sapiens
Description: PopHumanScan is a catalog about thousands of regions of the human genome showing evidences of selection along the human lineage. This database retrieved the population genomic d...Show Details...
Description: PLSDB is a database about bacterial plasmids retrieved from the NCBI nucleotide database. Users can select plasmids by various parameters such as the sequence length, topology, ...Show Details...
Database maintenance site: Faculdade de Medicina, Universidade de Lisboa
Organism(s) covered:All
Description: pATLAS is a database for searching plasmids with tools to visualize relationships between plasmids. Users can search plasmids by the name, taxa, antibiotic resistance and virule...Show Details...
Description: Catalyst Acquisition by Data Science (CADS) is an integrated visual platform for materials informatics. It provides three basic functions for users: 1) Data Management: CADS pro...Show Details...
Database maintenance site: Tokai University School of Medicine
Organism(s) covered:Eukaryota | Viruses
Description: pEVE is a database about predicted endogenous viral elements (EVEs) in eukaryotic genomes. It contains BLASTN search results of eukaryotic and viral genomes as target and query ...Show Details...
Description: JMC Primates Brain Imaging Repository is a collection of high-resolution MRI data of non-human primate brains stored in Japan Monkey Centre. Each record contains species informa...Show Details...
Description: Collagenseq is a reference database about type I collagen. Each record obtained from various species contains academic name and English name of the organism, taxonomy ID, and th...Show Details...
Description: LncRRIsearch is a web server for comprehensive prediction of interactions between long non-coding RNA (lncRNA)-lncRNA and lncRNA-mRNA in human and mouse. Users can also search T...Show Details...
Description: Cistrome DB is a portal site for public ChIP-seq and DNase-seq datasets. It provides a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data i...Show Details...
Description: CYCLoPs is a comprehensive database of protein abundance and localization for budding yeast Saccharomyces cerevisiae. It contains high resolution images covering about 75% of th...Show Details...
Description: YeastGFP is a database of yeast strains expressing full-length, chromosomally tagged green fluorescent protein (GFP) fusion proteins. It contains high-resolution, high-coverage ...Show Details...
Description: NGS-QC database is the first QC indicator database covering the largest collection of ChIP-seq and enrichment-related NGS datasets. Most of the current certified entries are par...Show Details...
Database maintenance site: University of Massachusetts Medical School
Organism(s) covered:Homo sapiens | Mus musculus
Description: Factorbook is a transcription factor (TF)-centric wiki-style repository of all ENCODE ChIP-seq datasets on TF-binding regions, as well as the rich analysis results of these data...Show Details...
Database maintenance site: Kazusa DNA Research Institute, National Institute of Genetics
Organism(s) covered:
Description: Food Metabolome Repository is a database for food metabolome data obtained using liquid chromatography-mass spectrometry (LC-MS). Each record contains a two-dimensional mass chr...Show Details...
Description: FMODB is a database of quantum mechanical data based on the FMO method. It contains PDBID-Chain (detail data of the displayed structure), IFIE SUM (Summation of ES, EX, CT+mix, ...Show Details...
Database maintenance site: Hiroshima University Amphibian Research Center
Organism(s) covered:Xenopus tropicalis
Description: XenoBiores maintains data collected from the NBRP Xenopus tropicalis Project to establish inbred and standard lines, as well as its supply. It contains information on biological...Show Details...
Description: toxRank is an application that provides a list of compounds those exhibit an expression profile similar to that of the genes inputted by user. This tool visualizes the clusterin...Show Details...
Description: toxBridge is a database that stores statistical analysis results using differential gene expression when compounds are exposed. It is possible to display feasible bridging capab...Show Details...
Database maintenance site: National Institutes of Biomedical Innovation, Health and Nutrition
Organism(s) covered:
Description: TOXPILOT is a system for visualization maps of toxic process ontology (TXPO) which systematizes terms involving toxicity courses and processes. It provides following search cate...Show Details...
Description: DILI-cSEARCH is a comprehensive database about liver toxicity caused by drugs and chemicals. It offers cross search access to information of Open TG-GATEs, DrugMatrix, LINKS and...Show Details...
Database maintenance site: National Institutes of Biomedical Innovation, Health and Nutrition
Organism(s) covered:rattus | Homo sapiens
Description: DILI-TOOLBOX is a portal site for liver toxicity database and prediction systems developed in the AMED Liver Toxicity Informatics System Development programs. It by the National...Show Details...
Description: piRTarBase is a database about PIWI-interacting RNAs (piRNAs) which are a class of small noncoding RNAs that guard animal genomes against mutation by silencing transposons. It p...Show Details...
Database maintenance site: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences
Organism(s) covered:Viridiplantae
Description: PED is a curated database of RNA editosome in plants, which is focused on the curation, integration and standardization of plant RNA editing factors (editosome) and the related ...Show Details...
Database maintenance site: Huazhong University of Science and Technology, UTHealth (University of Texas Health Science Center at Houston)
Organism(s) covered:Homo sapiens
Description: Pancan-meQTL is a database for systematically prediction about the effects of SNPs on methylation levels of human genome. It provides cis-meQTLs (SNPs affect local methylation l...Show Details...
Description: OpenProt is a database that enforces a polycistronic model of eukaryotic genome annotations. It annotates known proteins (RefProts), novel predicted isoforms (Isoforms) and nove...Show Details...
Database maintenance site: Peking University Cancer Hospital and Institute, Chinese Academy of Sciences, University of Michigan
Organism(s) covered:Homo sapiens
Description: OncoBase is an integrated database for annotating somatic mutations from more than 120 cancer projects. Data are collected from TCGA, ICGC, COSMIC and ClinVar.It provides compre...Show Details...
Description: NucMap is a database about genome-wide nucleosome positioning map of organisms. The nucleosome positioning information is provided by a single nucleotide resolution in every org...Show Details...
Database maintenance site: Cancer Science Institute of Singapore
Organism(s) covered:Homo sapiens | Mus musculus
Description: MethMotif is an integrative database of transcription factor binding motifs coupled with DNA methylation profiles using the results of ChIP-seq and Whole Genome Bisulfite Sequen...Show Details...
