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PCM-SABRE / Precision Cancer Medicine - Survival Analysis Benchmarking Reporting and Evaluation
Supports the entire knowledge discovery process for cancer outcome analysis. PCM-SABRE allows to compare and improve expression-based predictive models of cancer patients. It could be used to replicate previous work that describe predictive models of breast cancer recurrence, and evaluated the performance of all possible combinations of feature selection methods and data mining algorithms that was used in either of the works. It provides an intuitive environment for rapid development of predictive models in cancer precision medicine. PCM-SABRE was developed using KNIME.
GenTAC / Genetically triggered thoracic aortic condition
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Provides a biospecimen inventory and bioinformatics infrastructure to enable research to advance the clinical management of genetically triggered thoracic aortic aneurysms (TAAs) and related complications. GenTAC is a longitudinal observational cohort study enrolling patients with conditions related to genetically-induced TAAs from five regional clinical centers in the United States. GenTAC has been established to facilitate studies by GenTAC investigators and others that will advance multiple scientific frontiers in thoracic aortic disease.
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HbVar / Human Hemoglobin Variants and Thalassemias
Provides a locus-specific database. HbVar compiles information about genomic sequence changes leading to hemoglobin variants, hemoglobinopathies all types of thalassemia. The database gathers extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Besides, the tool was developed in interrelation with other databases, such as GALA, GenPhen and PhenCode.
Autism Chromosome Rearrangement Database
Gives access to a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature (databases and unpublished data). Autism Chromosome Rearrangement Database is continuously updated with information from in-house experimental data as well as data from published research studies. This resource aims to integrate multiple data sets in order to understand the full etiologic role of structural variation in autism spectrum disorder (ASD).
UK Biobank
Collects extensive phenotypic and genotypic detail about a very large, population-based prospective study. UK Biobank aims to encourage and provide as wide access as possible to its data and samples for health-related research in the public interest by all bona fide researchers from the academic, charity, public, and commercial sectors. The database aims to improve the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses – including cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression and forms of dementia.
SNCID / Stanley Neuropathology Consortium Integrative Database
A data-mining tool that includes 379 neuropathology data sets from hippocampus, as well as RNA-seq data measured in 15 well-matched cases in each of four groups: schizophrenia, bipolar disorder (BPD), major depression (MD) and unaffected controls. We analyzed the neuropathology data from the hippocampus to identify those abnormalities that are shared between psychiatric disorders and those that are specific to each disorder. The SNCID provides a unique opportunity to extensively profile thousands of neuropathology data sets from various brain regions that were measured in the same individuals with major psychiatric disorders.
F-SNP / The Functional Single Nucleotide Polymorphism database
Compiles computationally predicted functional information about Single Nucleotide Polymorphism (SNPs). F-SNP aims to simplify identification of disease-causing SNPs in association studies. The database is composed of four parts: (i) protein coding, (ii) splicing regulation, (iii)transcriptional regulation and (iv) post-translation. It includes the functional information for over 559 000 SNPs in 18 282 genes relevant to 85 major human diseases.
SNPeffect
Provides information about phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect is a database that allows users to search SNVs by filtering on molecular phenotypic effects, mutation type, disease, UniProt identifier, dbSNP identifier and gene name. Users can also analyze and plot phenotypic features of a specific subset (or all) of the SNPeffect database. It also includes a data submission framework for submitting (human or non-human) custom single protein variants for a detailed SNPeffect analysis including TANGO, WALTZ, LIMBO and FoldX.
AutismKB
A comprehensive knowledgebase of autism-related genes, CNVs and linkage regions with extensive evidence and annotations. AutismKB supports both text-based search and sequence-based search. Users can find a quick search box on the top right of each page to search by gene symbol. Advanced search was provided to search genes, CNVs, linkage regions by gene name, gene symbol, NCBI Entrez id, Ensemble id, GO terms, UniProt ID, location, score, method and PubMed ID. Finally, a BLAST search against the nucleotide or protein sequences of all AutismKB genes is also available.
PGDB / Human Prostate Gene DataBase
Offers a non-redundant catalog of genes involved in the prostate. PGDB covers genes involved in a number of molecular and genetic events of the prostate including gene amplification, mutation, gross deletion, methylation, polymorphism, linkage and over-expression, as published in the literature. It also provides inclusive and highly relevant supporting evidence from published literature. Users can query the database using gene names, symbols, aliases and identification numbers such as LocusLink ID or UniGene ID.
CADgene / Coronary Artery Disease Gene Database
Collects coronary artery disease (CAD) candidate genes and their detailed evidence associated with CAD from publications. CADgene is a comprehensive database that provides three approaches for searching the data, including the text search and sequence search. For each candidate gene, CADgene displays its involved KEGG pathways and all the CAD-related genes in these pathways. The database aims to provide a complete and up-to-date gene resource to the research community.
DAA / Digital Ageing Atlas
Integrates molecular, physiological, psychological and pathological age-related data to create an interactive portal that serves as a centralised collection of human ageing changes and pathologies. The Digital Ageing Atlas (DAA) is a portal of age-related changes covering different biological levels. This database provides a centralised source for ageing-related data as well as basic tools to query and visualize the data, including anatomical models. It focuses on human ageing, but also includes supplementary mouse data, in particular gene expression data, to enhance and expand the information on human ageing.
Colorectal cancer atlas
An integrated web-based resource that catalogues the genomic and proteomic annotations identified in colorectal cancer (CRC) tissues and cell lines. The data catalogued to-date include sequence variations as well as quantitative and non-quantitative protein expression data. The database enables the analysis of these data in the context of signaling pathways, protein–protein interactions, Gene Ontology terms, protein domains and post-translational modifications. Currently, Colorectal Cancer Atlas contains data for >13 711 CRC tissues, >165 CRC cell lines, 62 251 protein identifications, >8.3 million MS/MS spectra, >18 410 genes with sequence variations (404 278 entries) and 351 pathways with sequence variants. Overall, Colorectal Cancer Atlas has been designed to serve as a central resource to facilitate research in CRC.
DIDA / DIgenic diseases DAtabase
Provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. DIDA currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided.
ARVD/C genetic variants database / Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy genetic variants database
Contains information from clinical research and other types of data on variants in genes causing arrhythmogenic right ventricular dysplasia/cardiomyopathy. ARVD/C genetic variants database is a comprehensive collection of arrhythmogenic cardiomyopathy (ACM) genetic data. It represents a source of information on the spectrum of ACM-associated genes and aims to facilitate the interpretation of genetic data and genetic counseling.
LongevityMap
Allows users to query genes, variants (including by reference single nucleotide polymorphism (SNP) ID number), studies, and cytogenetic locations. LongevityMap is a catalogue of human genetic variants associated with longevity, to serve as a reference to help researchers navigate the rising tide of data related to human longevity. This resource is an inclusive database in which both large and small studies are included; different types of study are featured, from cross-sectional studies to studies of extreme longevity.
DMDM / Domain Mapping of Disease Mutations
Provides an aggregated view of all human coding disease-related mutations and SNPs for each protein domain. To build DMDM, all human proteins were aligned to a database of conserved protein domains using a Hidden Markov Model-based sequence alignment tool (HMMer). The resulting protein-domain alignments were used to provide a domain location for all available human disease mutations and polymorphisms. The number of disease mutations and polymorphisms in each domain position are displayed alongside other relevant functional information (e.g. the binding and catalytic activity of the site and the conservation of that domain location). DMDM's protein domain view highlights molecular relationships among mutations from different diseases that might not be clearly observed with traditional gene-centric visualization tools. This domain-centric database provides an ideal framework for studying biological processes relevant to human health, as well as for the integration of other molecular events, such as protein translational modifications and alternative splicing events affecting protein domains.
IthaGenes / Interactive archive of all sequence variations affecting haemoglobin disorders
Provides a knowledgebase dealing with haemoglobin (Hb) disorders. IthaGenes is a curated database compiling about 2600 variations in over 230 genes including specifications about phenotype and epidemiology data as well as related publications. Information is organized according to three functional categories: globin-gene causative mutations, disease modifying mutations and relevant neutral polymorphisms.
GenDR
Provides a curated list of genes essential for dietary restriction (DR). GenDR contains a broad range of genes thank to its inclusive selection criteria. It can be used as an informational website and as a research tool. The database is composed of genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR, and genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals.
AD&FTDMDB / Alzheimer Disease & Frontotemporal Dementia Mutation Database
Aims at collecting all known mutations and non-pathogenic coding variations in the genes related to Alzheimer disease (AD) and frontotemporal dementia (FTD). AD&FTDMDB is updated continuously and contains mutations reported in the literature and at scientific meetings, and unpublished mutations directly submitted to the database. AD&FTDMDB allows to retrieve mutations based on the gene, phenotype and publication. Mutations are described at the genomic, mRNA and protein level. For each mutation, the number of unrelated patients/families is recorded and family details are available. Also, citations to the original publications are given with a link to their NLM PubMed record if available. Polymorphisms with a predicted effect on the protein level are also collected.
CFTR-France
Provides genetic information contents on the Cystic Fibrosis (CF) phenotype. The main objectives of CFTR-France were: (i) to collect all types of genetic data in each category of individuals who are extensively genotyped by the expert laboratories; (ii) to collect the associated clinical information available in laboratories; (iii) to collect epidemiological data in participating laboratories from the general population; and (iv) to analyze any data available in the literature concerning the clinical liability of variants using clinical descriptions, familial and epidemiological data.
BalbiEtAl2017
Provides high throughput datasets of stem cells. This database aims to model protein expression, particularly transcription factor (TF) expression, across multiple layers of stem cell regulation. The simulation model supports the argument that critically branching processes in cistromes can drive sub-critically branching processes in other cistromes to criticality. It is currently aspatial, in that it lacks any detail of three-dimensional genomic architecture, which affects how TFs access their binding sites.
GMTV / Genome-wide Mycobacterium tuberculosis variation
Gathers information about M. tuberculosis. GMTV includes clinical, epidemiological and microbiological description with genome variations based on whole genome sequencing data. It contains the whole genome sequences of more than 1000 M. tuberculosis isolates with various medical datasets from different regions. Besides, the database allows users to run association analysis between molecular variation and clinical consequences and aims to make easier the epidemiological surveillance of TB and HIV/TB co-infection.
AGEID / Aging genes/interventions database
Presents data related to the study of aging. AGEID is a database that catalogues, in one location, every published experiment where life span has been measured in any organism. It provides (i) formatted gene/intervention reports that contain the organism and strain background in which the particular experiment was performed, (ii) the type of genetic or environmental perturbation, (iii) the effect on life span, (iv) a description of the gene function and (v) its role in longevity, protein homologs, and references.
Orphanet
Aims to help improve the diagnosis, care and treatment of patients with rare diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, for all audiences. Orphanet offers a range of freely accessible services like an inventory of rare diseases and a classification of diseases elaborated using existing published expert classifications, an encyclopaedia of rare diseases in English and French, an inventory of orphan drugs at all stages of development, and an assistance-to-diagnosis tool allowing users to search by signs and symptoms and many others.
dbAARD / database of Aging and Age Related Disorders
A freely accessible interactive database of the relationships of human single nucleotide polymorphisms (SNPs) and age-related disorders along with the supporting evidence. dbAARD facilitates access to and analysis of the relationships asserted between human variation and observed disease conditions. dbAARD collects disease-SNP associations as well as their significance scores in the form of p-value and odds ratio. dbAARD collects disease-SNP associations asserted in GWAS reports as well as their significance scores in the form of p-value or odds ratio. This information is compiled from various publicly available databases like the NHGRI GWAS catalogue, GWAS Central, OMIM, HGMD and others, as well as literature searches. The alleles described in the reports are mapped to reference sequences, and reported according to the HGVS standard.
OCDB / OCD Database
A manually curated database collecting the relations between candidate genes in OCD, microRNAs (miRNAs) involved in the pathophysiology of OCD and drugs used in its treatments. For each gene, the bibliographic references with a brief description of the gene and the experimental conditions are shown. The database also lists the polymorphisms within genes and its chromosomal regions. OCDB data is enriched with both validated and predicted miRNA-target and drug-target information. The transcription factors regulations, which are also included, are taken from David and TransmiR. Moreover, a scoring function ranks the relevance of data in the OCDB context. The database is also integrated with the main online resources (PubMed, Entrez-gene, HGNC, dbSNP, DrugBank, miRBase, PubChem, Kegg, Disease-ontology and ChEBI). The web interface has been developed using phpMyAdmin and Bootstrap software. This allows (i) to browse data by category and (ii) to navigate in the database by searching genes, miRNAs, drugs, SNPs, regions, drug targets and articles. The data can be exported in textual format as well as the whole database in.sql or tabular format.
dbPEC / Database for Preeclampsia
Serves as a robust and regularly updated resource of assembled preeclampsia phenotypes and associated genes. We designed the user interface of dbPEC for easy navigation and the results pages are visually supported by color coded labels and charts. We included gene sets associated with severity, concurrent conditions, tissue sources and networks. The published scientific literature is the primary repository for all information documenting human disease. We used semantic data mining to retrieve and extract the articles pertaining to preeclampsia-associated genes and performed manual curation. We deposited the articles, genes, preeclampsia phenotypes and other supporting information into the dbPEC. It is publicly available and freely accessible.
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