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http://wpicr.wpic.pitt.edu/WPICCompGen/genomic_control/genomic_control.htm

Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software)

Proper citation: GC/GCF (RRID:SCR_009075) Copy   

•   Source: SciCrunch Registry

http://www.molecularbrain.org/

MolecularBrain is an attempt to collect, collates, analyze and present the microarray derived gene expression data from various brain regions side by side. Transcription Profile of any gene in Mouse (online) and Human Brain (not yet) can be accessed as a histogram along with links to access various aspects of that gene. The expression levels were calculated from microarray data deposited at GEO (Gene expression omnibus). The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Gene information along with their expression values can be also accessed from the alphabetical list of gene symbols on the footer. The protocol and GEO sample information is available.

Proper citation: Molecular Brain: Transcription Profiles of Mouse and Human Brains (RRID:SCR_008689) Copy   

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http://pingstudy.ucsd.edu/

A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu.

Proper citation: Pediatric Imaging Neurocognition and Genetics (RRID:SCR_008953) Copy   

•   Source: SciCrunch Registry

http://netage-project.org/

Database that contains gene sets and microRNA-regulated protein-protein interaction networks for longevity, age-related diseases and aging-associated processes.

Proper citation: NetAge Database (RRID:SCR_010224) Copy   

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http://wpicr.wpic.pitt.edu/WPICCompGen/newcovibd/covibd.htm

Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software)

Proper citation: COVIBD (RRID:SCR_009155) Copy   

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http://systers.molgen.mpg.de/

SYSTERS is a database of protein sequences grouped into homologous families and superfamilies. The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Gene, Human, Vertebrate, Genome, Human ORFs

Proper citation: SYSTERS (RRID:SCR_007955) Copy   

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http://interactome-cmp.ucsf.edu/

This database currently holds E-MAP scores (individual interactions and correlation coefficients) for budding yeast genes involved in the early secretory pathway and chromosome function (including DNA damage and repair, transcriptional control, chromosome segregation and telomere regulation). E-MAPs (Epistatic Mini Array Profiles) are formed by creating and quantifying high-density genetic interaction maps. With this method, observed double mutant colony sizes are compared to those that would be expected from a distribution of typical double mutant colonies of each strain. Each interaction is assigned a score, which indicates the magnitude of the difference from the expected value and the certainty of the score. Negative (or aggravating) scores (< -2.5) correspond to synthetic sick/lethal interactions while positive (or alleviating) scores (> +2.5) corresponds to epistatic or suppressor interactions.

Proper citation: Krogan Lab Interactome Database (RRID:SCR_008121) Copy   

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http://escience.invitrogen.com/ipath/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. LINNEA Pathways is a user-friendly comprehensive online resource for gene- or protein-based scientific research. It is based on a total of 248 signaling and metabolic human biological pathway maps created for Invitrogen by GeneGo. The current version of iPath features 225 maps displaying human regulatory and metabolic pathways established in experimental literature produced by MetaCore from GeneGo, Inc. The map objects (proteins, genes, EC functions, and compounds) are connected via metabolic transformations and physical protein interactions, which were assembled by the GeneGo team of experienced annotators, geneticists, and biochemists. The pathways are organized in a vertical fashion following the general signaling path from signaling molecules and membrane receptors, via signal transduction cascades, to transcription factors and their gene targets. Following the natural organization of cellular machinery with highly interconnected pathways and modules, many maps are linked together via hyperlinked box symbols. Such linkage allows the reconstruction of a big picture view of human cell biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Invitrogen iPath (RRID:SCR_008120) Copy   

•   Source: SciCrunch Registry

http://itfp.biosino.org/itfp/

ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page.

Proper citation: Intergrated Transcription Factor Platform (RRID:SCR_008119) Copy   

•   Source: SciCrunch Registry

http://www.ingenuity.com/

A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .

Proper citation: Ingenuity Pathways Knowledge Base (RRID:SCR_008117) Copy   

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http://microbialgenomics.energy.gov/index.shtml

Through its Microbial Genome Program (MGP) and its Genomics:GTL (GTL) program, DOEs Office of Biological and Environmental Research (BER) has sequenced more than 485 microbial genomes and 30 microbial communities having specialized biological capabilities. Identifying these genes will help investigators discern how gene activities in whole living systems are orchestrated to solve myriad life challenges. The MGP was begun in 1994 as a spinoff from the Human Genome Program. The goal of the program was to sequence the genomes of a number of nonpathogenic microbes that would be useful in solving DOE''s mission challenges in environmental-waste cleanup, energy production, carbon cycling, and biotechnology. Past projects include microbial genome program, microbial cell project, and the Laboratory Science Program at the DOE Joint Genome Institute. The two ongoing projects are Genomics: GTL program and Community Sequencing Program at the DOE Joint Genome Institute. Sponsors: Site sponsored by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Microbial Genomics Program (RRID:SCR_008140) Copy   

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http://www.ebi.ac.uk/ipd/mhc/bola/

This website is intended to be the definitive source of information on the bovine major histocompatibility complex - its genes, proteins and polymorphism. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The BoLA nomenclature committee is a standing committee of the International Society for Animal Genetics. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The information gathered here is based on the BoLA workshop reports, which are published in Animal Genetics and the European Journal of Immunogenetics. The workshop report data are reproduced with the permission of the publishers Blackwell Science, and other text on the site is used with the permission of CRC Press.

Proper citation: BoLA Nomenclature: International Society for Animal Genetics (RRID:SCR_008142) Copy   

•   Source: SciCrunch Registry

http://skonops.imbb.forth.gr/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance.

Proper citation: AnoBase: An Anopheles database (RRID:SCR_008166) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/asd/altsplice/index.html

AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases

Proper citation: AltSplice Database of Alternative Spliced Events (RRID:SCR_008162) Copy   

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http://www.ebi.ac.uk/asd/aedb/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs.

Proper citation: Alternative Exon Database (RRID:SCR_008157) Copy   

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http://csbdb.mpimp-golm.mpg.de/

CSB.DB presents the results of bio-statistical analysis on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life''s complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The main focus of the CSB project is the generation of new easily accessible knowledge about the relationship and the hierarchy of cellular components. Thus new progress towards understanding lifes complexity pyramid is made. For this aim statistical and computational algorithms are applied to organism specific data derived from publicly available multi-parallel technologies, currently such as expression profiles. The underlying data are derived from various research activities. Thus CSB project provides an integrated and centralized public resource allowing universal access on the generated knowledge CSB.DB: A Comprehensive Systems-Biology Database. The derived knowledge should support the formulation of new hypotheses about the respective functional involvement of genes beyond their (inter-) relationships. Another major goal of the CSB project is to supply the researchers with necessary information to formulate these new hypotheses without demanding any a-priori statistical knowledge of the user. The CSB project mainly focuses on application of required statistical tests as well as to assist the user during exploration of results with information / help files to support hypothesis generation

Proper citation: Comprehensive Systems-Biology Database (RRID:SCR_008185) Copy   

•   Source: SciCrunch Registry

http://chromium.lovd.nl/LOVD2/home.php?select_db=CDKN2A

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The CDKN2A Database presents the germline and somatic variants of the CDKN2A tumor suppressor gene recorded in human disease through June 2003, annotated with evolutionary, structural, and functional information, in a format that allows the user to either download it or manipulate it for their purposes online. The goal is to provide a database that can be used as a resource by researchers and geneticists and that aids in the interpretation of CDKN2A missense variants. Most online mutation databases present flat files that cannot be manipulated, are often incomplete, and have varying degrees of annotation that may or may not help to interpret the data. They hope to use CDKN2A as a prototype for integrating computational and laboratory data to help interpret variants in other cancer-related genes and other single nucleotide polymorphisms (SNPs) found throughout the genome. Another goal of the lab is to interpret the functional and disease significance of missense variants in cancer susceptibility genes. Eventually, these results will be relevant to the interpretation of single nucleotide polymorphisms (SNPs) in general. The CDKN2A locus is a valuable model for assessing relationships among variation, structure, function, and disease because: Variants of this gene are associated with hereditary cancer: Familial Melanoma (and related syndromes); somatic alterations play a role in carcinogenesis; allelic variants occur whose functional consequences are unknown; reliable functional assays exist; and crystal structure is known. All variants in the database are recorded according to the nomenclature guidelines as outlined by the Human Genome Variation Society. This database is currently designed for research purposes only and is not yet recommended as a clinical resource. Many of the mutations reported here have not been tested for disease association and may represent normal, non-disease causing polymorphisms.

Proper citation: CDKN2A Database (RRID:SCR_008179) Copy   

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http://jbirc.jbic.or.jp/hinv/ppi/

The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project. The PPI view is now providing 32,198 human PPIs comprised of 9,268 H-InvDB proteins. H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. Sponsors: This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program.

Proper citation: H-Invitational Database: Protein-Protein Interaction Viewer (RRID:SCR_008054) Copy   

•   Source: SciCrunch Registry

http://www.rhesusbase.org/drugDisc/CAM.jsp

OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families. Totally 496 human CAM genes were compiled and annotated. We have mapped these genes onto a novel cell adhesion molecule ontology (CAMO) that provides a hierarchical description of cell adhesion molecules and their functions. It is intended to provide a means to facilitate better and better understanding of the global and specific properties of CAMs through their genomic features, regulatory modes, expression patterns and disease associations become clearer. You may browse by CAM ontology, Chromosomes and Full Gene list.

Proper citation: OKCAM: Ontology-based Knowledgebase for Cell Adhesion Molecules (RRID:SCR_010696) Copy   

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http://www.snps3d.org/

A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.

Proper citation: SNPs3D (RRID:SCR_010787) Copy   

•   Source: SciCrunch Registry