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http://zfishbook.org/

Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.

Proper citation: zfishbook (RRID:SCR_006896) Copy   

•   Source: SciCrunch Registry

http://www.stat.cmu.edu/~roeder/=ettdt/

Software application (entry from Genetic Analysis Software)

Proper citation: ET-TDT (RRID:SCR_007657) Copy   

•   Source: SciCrunch Registry

http://www.niaaa.nih.gov/research/major-initiatives/collaborative-studies-genetics-alcoholism-coga-study

Database and biorepository from a multi-site, multi-disciplinary study characterizing the familial transmission of alcoholism and related phenotypes and identifying susceptibility genes using genetic linkage. Investigators have assembled a collection of over 300 extended families densely affected by alcoholism (more than 3000 individuals), including clinical, neuropsychological, electrophysiological, biochemical, and genetic data, and established a repository of immortalized cell lines from these individuals, to serve as a permanent source of DNA for genetic studies. NIAAA has funded the Collaborative Studies on Genetics of Alcoholism (COGA) since 1989, with the goal of identifying the specific genes underlying this vulnerability. Data and biomaterials are available to qualified investigators in the broader scientific community. Recipients of data and biomaterials will be responsible for defraying the cost of their distribution. Pedigrees densely affected with alcoholism (DSM-III-R) have been ascertained at six sites (SUNY Downstate Health Sciences Center, University of Connecticut, Indiana University, Washington University, University of Iowa, and The University of California at San Diego). Diagnoses of alcohol dependence according to several diagnostic systems (e.g., DSM-III-R, Feighner, ICD-10) are made based on examination of medical records and direct assessment using the Semi-Structured Assessment for Genetics of Alcoholism (SSAGA). Nuclear and extended pedigrees containing at least two alcohol-dependent first-degree relatives in addition to an alcohol dependent proband (with all affected individuals meeting both DSM-IIIR and Feighner criteria) have been ascertained. Clinical data comprises anonymous data on family structure, age, sex, vital status, psychopathology, diagnosis, other clinically relevant information, are stored, maintained, and distributed by Washington University. Research data, consist of data on blood biochemistry and psychological test performance, which are stored, maintained, and distributed by Washington University, and brain electrophysiological data, which are stored, maintained, and distributed by SUNY. Genetic analysis data, consisting of marker genotypes, along with results of previous genetic analyses of COGA data, are stored, maintained, and distributed by Washington University. Biomaterials, consisting of lymphoblastoid cell lines and DNA from participating subjects are stored, maintained, and distributed by Rutgers University. Researchers may gain access to clinical data, research data, genetic analysis data, and biomaterials, subject to NIAAA approval, by completing an application details available from the website. After access certification, the principal investigator will be given access to electronic data files and other documentation.

Proper citation: Collaborative Studies on Genetics of Alcoholism (RRID:SCR_006841) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/BEAM/

Software application that treats the disease-associated markers and their interactions via a bayesian partitioning model and computes, via Markov chain Monte Carlo, the posterior probability that each marker set is associated with the disease. (entry from Genetic Analysis Software)

Proper citation: BEAM (RRID:SCR_007258) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/ldSelect.html

Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LDSELECT (RRID:SCR_007010) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/INTEGRAYEDMAP.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data.

Proper citation: INTEGRAYEDMAP (RRID:SCR_007489) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/LDMAP

Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software)

Proper citation: LDMAP (RRID:SCR_006308) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://ckb.jax.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.gcbi.com.cn

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   

•   Source: SciCrunch Registry

http://catlas.org/mousebrain/#!/

Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans.

Proper citation: CATlas (RRID:SCR_018690) Copy   

•   Source: SciCrunch Registry

https://www.sdu.dk/da/Om_SDU/Institutter_centre/Ist_sundhedstjenesteforsk/Centre/DTR.aspx?sideid=index&sprog=eng

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   

•   Source: SciCrunch Registry

http://epifactors.autosome.ru/

Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.

Proper citation: EpiFactors (RRID:SCR_016956) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://cometa.tigem.it/

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   

•   Source: SciCrunch Registry

http://mouse.brain-map.org/

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   

•   Source: SciCrunch Registry