Technological advances have greatly increased the availability of human genomic sequencing. However, the capacity to analyze genomic data in a clinically meaningful way lags behind the ability to generate such data.
Offers an online catalog of human genes and genetic disorders. OMIM integrates genomic coordinate searches of the gene map, views of genetic heterogeneity of phenotypes, and side-by-side comparisons of clinical synopses. It focuses on the molecular relationship between genetic variation and phenotypic expression. This database is based on the published peer-reviewed biomedical literature. It is useful for clinicians, molecular biologists and genome scientists.
Provides a resource that can be utilized for clinical, genomic, transcriptomic and functional analyses of acute myeloid leukaemia (AML) biology. Vizome is an online data browser that offers expression-signature heat maps for drug. It also includes a workflow in which the data normalization, curve fit parameters and quality assurance/quality control steps are summarized.
Provides germline and somatic variants of any size, type or genomic location. ClinVar gathers interpretations of clinical significance of variants for reported conditions. It accepts submissions from clinical testing labs, researchers, locus-specific databases, other databases, expert panels and groups establishing professional guidelines from all countries. This database offers general and advanced query interfaces.
Permits the identification of active long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), messenger RNA (mRNA) interactions. LncACTdb can also be used for dissecting the competing endogenous RNAs (ceRNAs) regulation in various cancers and identifying novel cancer biomarkers. Moreover, this resource provides confidential resources for researchers. Furthermore, it can supply illustration of survival, network and cancer hallmark information.
Covers mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected The Cancer Genome Atlas (TCGA) tumor samples. LinkedOmics harbors multi-omics data and clinical data for mover than 30 cancer types and of over 11 000 patients from the TCGA project. This database is available on a platform that offers three data analysis modules: LinkFinder, LinkCompare, and LinkInterpreter.
Compiles information related to precision medicine. PreMedKB consists of a repository organized around four main components : (i) genes, (ii) variants, (iii) drugs, and (iv) diseases. Users are allowed to search and retrieve all relationships between these components.This program can be used for providing precision treatment options in order to elaborate a clinical decision or to identify genomic risk factors.
Gathers genetic, genomic, and clinical knowledge of coding variants in the human genome. VarCards accelerates the prioritization of candidate variations and genes. It offers a web interface to search, browse and annotate the variant and gene-level implications of any given coding variants. This database is composed of about 110 155 000 single nucleotide variants (SNVs) and 1 223 000 insertions and deletions (INDELs) in coding regions or splicing sites.
A manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions. All conditions with identified genetic causes are included in the CGD. For each entry, the database includes the gene symbol, condition(s), allelic conditions, inheritance, age (pediatric or adult) in which interventions are indicated, clinical categorization, and a general description of interventions/rationale. The contents are not intended to serve as nor substitute for comprehensive clinical guidelines, but are rather intended to briefly describe the types of interventions that might be considered.
A National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genomic variants for use in precision medicine and research. ClinGen will engage the genomics community in data sharing efforts, develop the infrastructure and standards to support curation activities, and incorporate machine-learning approaches to speed the identification of clinically relevant variants.
Provides a registry for clinicians, genetic counselors, and researchers about dystrophic epidermolysis bullosa DEB patients and their associated COL7A1 mutations. The international dystrophic epidermolysis bullosa patient registry also collects data about the genotypes (i.e., the combinations of mutations in RDEB), patients, and clinical and molecular phenotypes in which they are involved. Lists contains all the phenotypes ever found in combination with a certain genotype including the reported exceptions to that most likely outcome.
Contains molecular and clinical data from thousands of patients and cell lines, along with tools for analysis and data visualization. G-DOC Plus enables the integrative analysis of multiple data types to understand disease mechanisms. The platform has three overlapping entry points for the user based on their interests: 1) Personalized Medicine, 2) Translational Research, and 3) Population Genetics. All data derives from studies on topics such as breast cancer, wound healing, or even 1,000 Genomes.
Allows users to browse clinically relevant associations deduced from The Cancer Genome Atlas (TCGA) data. The Cancer Genome Atlas Clinical Explorer consists of three main panels: (1) a search engine to identify genes associated to a targeted clinical parameter (2) a search engine for genomic or proteomic profile changes; and (3) a testing two-hit hypothesis test. This platform complements existing resources by supplying clinically oriented summaries.
Allows to genetic diversity in human populations. HGDP has collected genomic DNA from 1,043 individuals from around the world and has determined their genotypes at more than 650,000 single nucleotide polymorphism (SNP) loci. It represents 51 different populations from Africa, Europe, the Middle East, South and Central Asia, East Asia, Oceania and the Americas. The database shares ancestry and admixture, relationships between haplotype heterozygosity and geography, and population differences in copy number variation (CNV) throughout the human genome in the 1,043 individuals.
Stores all the genes and related molecular signatures that are involved in squamous cell carcinoma (ESCC) based on an exhaustive literature survey. ESCC ATLAS consists of an in-depth resource of gene, miRNA and protein information and their relationships to ESCC overall and in a population specific manner. It is useful for the discovery of novel anticancer drugs targeting the ESCC, or for understanding the ESCC pathogenesis.
Combines a relational database with various functions that can be directly queried online and shared by users. UMD-CFTR is a database designed for extensive collection and analysis of disease-causing mutations, polymorphisms, and unclassified variants. This resource offers, for patients who have been explored for all Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) coding/flanking sequences, the possibility to record and analyze any variations that have been found for each allele in cis and in trans.
Focuses on issues specific to the study of antigenic variation that are common across gene families. varDB aims to serve as a workspace, comprising analytical tools and sequence management facilities, with various options for downloading and uploading individual datasets into private accounts for logged-in users. This database is a resource where different antigenically variant gene families can be obtained and analyzed simultaneously.
A tool for interactively exploring survival correlations, and for downloading clinical data coupled to expression data for mRNAs, miRNAs, or lncRNAs. OncoLnc contains survival data for 8,647 patients from 21 cancer studies performed by The Cancer Genome Atlas (TCGA), along with RNA-seq expression for mRNAs and miRNAs from TCGA, and lncRNA expression from MiTranscriptome beta. Storing this data gives users the ability to separate patients by gene expression, and then create publication-quality Kaplan-Meier plots or download the data for further analyses. OncoLnc also stores precomputed survival analyses, allowing users to quickly explore survival correlations for up to 21 cancers in a single click.
Contains a comprehensive resource about genes and related cancer prognosis. RTPDB includes more of 700 studies, which consist of single nucleotide polymorphism (SNP) studies of almost 60 000 patients with genes, tumors and treatment types, and 500 expression studies with more of 55 000 patients and their genes, tumors and treatment types. The names of genes and their variants were converted and displayed in the form of the official symbol. The detailed information of the tumor, treatment and prognosis were also classified.
Provides information about clinical cancer variants and interpretations in a structured way. PMKB is an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. The database contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. The interpretations are accessed either directly via the Web interface or programmatically via the existing application programming interface (API).
Informs users on the associations of single nucleotide polymorphisms (SNPs) with esophageal squamous-cell carcinoma (ESCC) risk. CCGD-ESCC is an online database that gathers data about survival time of ESCC patients (survival genome-wide association study (GWAS)) and gene expression (expression quantitative trait loci, expression quantitative trait loci (eQTL)). This resource permits users to observe evidence between somatic mutations and survival time in ESCC patients.