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http://cgap.nci.nih.gov/Chromosomes/Mitelman
The web site includes genomic data for humans and mice, including transcript sequence, gene expression patterns, single-nucleotide polymorphisms, clone resources, and cytogenetic information. Descriptions of the methods and reagents used in deriving the CGAP datasets are also provided. An extensive suite of informatics tools facilitates queries and analysis of the CGAP data by the community. One of the newest features of the CGAP web site is an electronic version of the Mitelman Database of Chromosome Aberrations in Cancer. The data in the Mitelman Database is manually culled from the literature and subsequently organized into three distinct sub-databases, as follows: -The sub-database of cases contains the data that relates chromosomal aberrations to specific tumor characteristics in individual patient cases. It can be searched using either the Cases Quick Searcher or the Cases Full Searcher. -The sub-database of molecular biology and clinical associations contains no data from individual patient cases. Instead, the data is pulled from studies with distinct information about: -Molecular biology associations that relate chromosomal aberrations and tumor histologies to genomic sequence data, typically genes rearranged as a consequence of structural chromosome changes. -Clinical associations that relate chromosomal aberrations and/or gene rearrangements and tumor histologies to clinical variables, such as prognosis, tumor grade, and patient characteristics. It can be searched using the Molecular Biology and Clinical (MBC) Associations Searcher -The reference sub-database contains all the references culled from the literature i.e., the sum of the references from the cases and the molecular biology and clinical associations. It can be searched using the Reference Searcher. CGAP has developed six web search tools to help you analyze the information within the Mitelman Database: -The Cases Quick Searcher allows you to query the individual patient cases using the four major fields: aberration, breakpoint, morphology, and topography. -The Cases Full Searcher permits a more detailed search of the same individual patient cases as above, by including more cytogenetic field choices and adding search fields for patient characteristics and references. -The Molecular Biology Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to gene rearrangements as a consequence of cytogenetic aberrations. -The Clinical Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to clinical associations of cytogenetic aberrations and/or gene rearrangements. -The Recurrent Chromosome Aberrations Searcher provides a way to search for structural and numerical abnormalities that are recurrent, i.e., present in two or more cases with the same morphology and topography. -The Reference Searcher queries only the references themselves, i.e., the references from the individual cases and the molecular biology and clinical associations. Sponsors: This database is sponsored by the University of Lund, Sweden and have support from the Swedish Cancer Society and the Swedish Children''s Cancer Foundation
Proper citation: Mitelman Database of Chromosome Aberrations in Cancer (RRID:SCR_012877) Copy
http://biome.ewha.ac.kr:8080/GSEAWebApp/
An integrative platform for diverse types of gene set analysis with annotation network navigation. It includes tools for statistical analysis, visualization of annotation relationships, retrieval of genes from annotation database, and set operation for gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, they have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.
Proper citation: GARNET (RRID:SCR_012033) Copy
http://www.informatics.jax.org/
Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology.
Proper citation: Mouse Genome Database (RRID:SCR_012953) Copy
http://geneticassociationdb.nih.gov/
The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature. The data is from published scientific papers. Study data is recorded in the context of official human gene nomenclature with additional molecular reference numbers and links. It is gene centered. That is, each record is a record of a gene or marker. If a study investigated 6 genes for a particular disorder, there will be 6 records. Anyone may view this database and anyone may submit records. You do not have to be an author on the original study to submit a record. All submitted records will be reviewed before inclusion in the archive. Both genetic and environmental factors contribute to human diseases. Most common diseases are influenced by a large number of genetic and environmental factors, most of which individually have only a modest effect on the disease. Though genetic contributions are relatively well characterized for some monogenetic diseases, there has been no effort at curating the extensive list of environmental etiological factors. From a comprehensive search of the MeSH annotation of MEDLINE articles, they identified 3,342 environmental etiological factors associated with 3,159 diseases. They also identified 1,100 genes associated with 1,034 complex diseases from the NIH Genetic Association Database (GAD), a database of genetic association studies. 863 diseases have both genetic and environmental etiological factors available. Integrating genetic and environmental factors results in the etiome, which they define as the comprehensive compendium of disease etiology.
Proper citation: Genetic Association Database (RRID:SCR_013264) Copy
http://xin.cz3.nus.edu.sg/group/trmp/trmp.asp
The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore.
Proper citation: Therapeutically Relevant Multiple Pathways Database (RRID:SCR_013471) Copy
http://sbrg2.gist.ac.kr/hcnet/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A specialized database for mouse heart and calcium signaling toolkit genes. It contains the functional gene modules pre-calculated from the microarray data compendium using various algorithms for genetic network analyses. The Heart and Calcium functional Network (HCNet) database is a collection of functional gene clusters calculated from microarray data compendium obtained from the Korea Systems Biology Initiative and from the publicly available GEO database. It was designed to assist experimentalists especially in the field of cardiac and calcium signaling research to detect potential network motifs and gene clusters that are functionally related or co-regulated by common transcription factors. Genes of defined numbers are classified into two categories, 1) heart-specific genes and 2) heart-specific genes plus calcium signaling toolkit-genes.
Proper citation: Heart and Calcium Functional Network Database (RRID:SCR_013515) Copy
http://signal.salk.edu/cgi-bin/RiceGE
Gene database for Japonica rice. RiceGE is associated with SIGnAL at the Salk Institute.
Proper citation: RiceGE (RRID:SCR_015061) Copy
Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years.
Proper citation: Danish Twin Registry (RRID:SCR_017482) Copy
http://epifactors.autosome.ru/
Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.
Proper citation: EpiFactors (RRID:SCR_016956) Copy
Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions.
Proper citation: CoMeTa Website (RRID:SCR_017357) Copy
http://hb.flatironinstitute.org/
Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.
Proper citation: HumanBase (RRID:SCR_016145) Copy
Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain.
Proper citation: ABA Mouse Brain: Atlas (RRID:SCR_017479) Copy
Semi-automated and manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and oncology clinical trials. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials.
Proper citation: Jackson Laboratory Clinical Knowledgebase (RRID:SCR_014965) Copy
http://diabetes.wisc.edu/index.php
Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.
Proper citation: Attie Lab Diabetes Database (RRID:SCR_016639) Copy
http://software.broadinstitute.org/gsea/msigdb/index.jsp
Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.
Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy
http://www.informatics.jax.org/humanDisease.shtml
Collection of published and potential mouse models of human disease, discovery of candidate genes and investigation of phenotypic similarity between mouse models and human patients. Mouse mutation, and phenotype and disease model data from Mouse Genome Informatics database are integrated with human gene to disease relationships from the National Center for Biotechnology Information and Online Mendelian Inheritance in Man and human disease to phenotype relationships from the Human Phenotype Ontology.
Proper citation: Human Mouse Disease Connection (RRID:SCR_017522) Copy
Database provides information on research status of gene related diseases, gene expression in different tissues, regulatory relationship among genes, information of diseases, mRNA, Transcription Fctor, miRNA and other information shared among genes.
Proper citation: GCBI database (RRID:SCR_018971) Copy
https://hive.biochemistry.gwu.edu/dna.cgi?cmd=tissue_codon_usage&id=586358&mode=cocoputs
Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data.
Proper citation: Codon and Codon-Pair Usage Tables (RRID:SCR_018504) Copy
http://www.broadinstitute.org/pubs/MitoCarta/
Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.
Proper citation: MitoCarta (RRID:SCR_018165) Copy
Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class.
Proper citation: ResistomeDB (RRID:SCR_018305) Copy
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