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http://www.nibb.ac.jp/brish/indexE.html

Database of detailed protocols for single and double in situ hybridization (ISH) method, probes used by Yamamori lab and others useful for studies of brain, and many photos of mammalian (mostly mouse and monkey) brains stained with various gene probes. Also includes a brain atlas of gene expression. Currently, the atlas comprises a series of un-annotated images showing the localization of a particular probe or molecule, e.g., AChE.

Proper citation: BraInSitu: A homepage for molecular neuroanatomy (RRID:SCR_008081) Copy   

•   Source: SciCrunch Registry

http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html

The database HOX Pro contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes. The HOX-Pro database is aimed at: 1. analysis and classification of regulatory and coding regions in diverse homeobox and related genes; 2. describing mutations and knock-outs of hox-genes, as well as hereditary diseases related to these genes; 3. graphical representation, comparisons and classification of hox-genes expression patterns and profiles (sea urchin blastula, Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian brain, human EC cells); 4. comparative analysis of organization of hox-based genetic networks the nematode Caenorhabditis elegans the sea urchins Strongylocentrotus purpuratus and other echinids, the fruit flies Drosophila melanogaster and D.virilis, the vertebrates chicken and mouse; 5. analysis of phylogeny and evolution of homeobox genes and clusters. The HOX Pro contains a broad spectrum of information including images, diagrams and animations. Currently this amounts to approximately 700 html-pages together with 400 images which contain information on 200 groups of genes and 90 promoters, in turn linked to maps of 15 HOX clusters and 9 genetic networks. For today it is known about 700 sequences of individual hox-genes of animals classified approximately in 200 homologous or paralogous groups. The HOX Pro database contains data on the structural and functional organization of the transcriptional regulatory machinery of homeobox and functionally related genes. The hierarchical organization of transcription regulation of metazoan genes is incorporated into the database schema. HOX Pro includes a hypertext description of the mechanisms of homeobox gene activation as well as the functional characteristics of proteins encoded by homeobox-containing and functionally related genes.

Proper citation: HOX Pro (RRID:SCR_008115) Copy   

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http://dictybase.org

This website contains the genome sequence of Dictyostelium discoideum. The determination of the entire information content of the Dictyostelium genome will be of great value to those working with this organism directly, as well as to those who would like to determine the functions of homologous genes from other species. Dictyostelium discoideum, a soil-living amoeba, is an excellent organism for the study of the molecular mechanisms of cell motility, signal transduction, cell-type differentiation and developmental processes. Genes involved in any of these processes can be knocked-out rapidly by targeted homologous recombination. Since Dictyostelium is haploid, mutants are readily isolated and the REMI (restriction enzyme mediated integration) technique of insertional mutagenesis allows the facile cloning of disrupted genes. The Dictyostelium genome is being sequenced with the chromosomal shotgun methodology on a chromosome by chromosome basis. The six Dictyostelium chromosomes with sizes ranging from four to seven Mb are being separated by PFGE (Pulsed Field Gel Electrophoresis) by Edward Cox, Princeton University. Chromosomal libraries with insert sizes between 1 and 4 kb are being generated by the Sanger Centre using pUC18 as a vector. For shotgun sequencing both forward and reverse reads from each clone randomly selected from the chromosome-enriched libraries are being produced. The read pairs will represent a useful mapping resource to assess contig order. For every Mb of DNA an estimated number of 20,000 - 25,000 single shotgun reads will be necessary. The hereditary information is carried on 6 chromosomes with sizes ranging from 4 to 7 Mb resulting in a total of about 34 Mb of DNA, a multicopy 90 kb extrachromosomal element that harbours the rRNA genes, and the 55 kb mitochondrial genome. The estimated number of genes in the genome is 8,000 to 10,000 and many of the known genes show a high degree of sequence similarity to homologues in vertebrate species.

Proper citation: Dictyostelium discoideum genome database (RRID:SCR_008149) Copy   

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http://locus.jouy.inra.fr/cgi-bin/lgbc/mapping/common/intro2.pl?BASE=goat

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website contains information about the mapping of the caprine genome. It contains loci list, phenes list, cartography, gene list, and other sequence information about goats. This website contains 731 loci, 271 genes, and 1909 homologue loci on 112 species. It also allows users to summit their own data for Goatmap. ARK-Genomics is not-for-profit and has collaborators from all over the world with an interest in farm animal genomics and genetics. ARK-Genomics was initially set up in 2000 with a grant awarded from the BBSRC IGF (Investigating Gene Function) initiative and from core resources of the Roslin Institute to provide a laboratory for automated analysis of gene expression using state-of-the-art genomic facilities. Since then, ARK-Genomics has expanded considerably, building up considerable expertise and resources.

Proper citation: GoatMap Database (RRID:SCR_008144) Copy   

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http://wwwmgs.bionet.nsc.ru/mgs/gnw/about.shtml

GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses.

Proper citation: GeneNetWorks (RRID:SCR_008034) Copy   

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http://www.gene-regulation.com/pub/databases.html

In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes.

Proper citation: Gene Regulation Databases (RRID:SCR_008033) Copy   

•   Source: SciCrunch Registry

http://ncv.unl.edu/Angelettilab/HPV/Database.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 23, 2016. The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. It includes molecular biologists, sequence analysts, computer technicians, post-docs and graduate research assistants. This Web site has two main branches. The first contains our four annual data books of papillomavirus information, called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. and the second contains papillomavirus genetic sequence data. There is also a New Items location where we store the latest changes to the database or any other current news of interest. Besides the compendium, we also provide genetic sequence information for papilloma viruses and related cellular proteins. Each year they publish a compendium of papillomavirus information called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. which can now be downloaded from this Web site.

Proper citation: HPV Sequence Database (RRID:SCR_008154) Copy   

•   Source: SciCrunch Registry

http://www.genomatix.de/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 13,2026. Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc.

Proper citation: Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) Copy   

•   Source: SciCrunch Registry

https://plantcyc.org/databases/aracyc/15.0

Curated species-specific database present at the Plant Metabolic Network. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

Proper citation: AraCyc (RRID:SCR_008109) Copy   

•   Source: SciCrunch Registry

http://psychiatry.ucsd.edu/Neuroembryologylab/index.htm

Dr. Eric Turner''s laboratory studies the mechanisms underlying the development of the nervous system. The vertebrate brain is comprised of a tremendous variety of neurons, each class exhibiting a unique phenotype characterized by the expression of specific neurotransmitter receptors, ion channels, patterns of axonal growth, and synapse formation. The research we conduct focuses on the critical role transcription factors play in the specification of neuronal cell type during development. We are particularly interested in transcription factors of the homeodomain family that bind to DNA and in doing so activate or repress gene expression. One area of study is the role of POU-domain transciption factor Brn3a in axon growth and survival. The primary research areas are: * Neuronal cell fate determination: The expression of regulatory genes is manipulated in living chick embryos using microsurgery and electroporation and the effects on neural marker genes studied. * Molecular mechanisms of gene regulation: Target DNA binding sites of neural transcription factors are biochemically characterized and findings coordinated with sequence data from the mouse and human genomes. * Targeted misexpression of regulatory genes: Transgenic and knockout mouse technology is used to misexpress genes of interest, and the effects on neural marker genes, axonal growth, and cell survival studied. * Global analysis of neural gene expression: Micro-arrays (GeneChips) are employed in conjunction with other areas of study to understand the coordinated regulation of gene expression in the nervous system. Dr. Turner is a member of the University of California, San Diego''s Graduate Program in Neuroscience and Biomedical Sciences Program and accepts students from these two programs. Interesting rotation projects are available using methods ranging from biochemistry and molecular biology to embryology. Additionally, Dr. Turner is also the Director of this NIMH-funded training program for research-oriented psychiatrists, psychologists, and basic neuroscientists working in areas relevant to psychiatry. Typically Fellows spend two years in the program, during which they develop a research project under the close supervision of one of the highly productive members of the UCSD Department of Psychiatry, or another investigator in the La Jolla (UCSD/Salk/Scripps) research community.

Proper citation: Department of Psychiatry, Turner Laboratory (RRID:SCR_008067) Copy   

•   Source: SciCrunch Registry

http://genewindow.nci.nih.gov/

Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible

Proper citation: GeneWindow (RRID:SCR_008183) Copy   

•   Source: SciCrunch Registry

http://www.osc.riken.jp/english/

Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level.

Proper citation: RIKEN Omics Science Center (RRID:SCR_008241) Copy   

•   Source: SciCrunch Registry

http://www.repairgenes.org/index.shtml

The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system.

Proper citation: repairGenes (RRID:SCR_008240) Copy   

•   Source: SciCrunch Registry

http://gfpweb.aecom.yu.edu/

Provided here is a database of expression patterns of C. elegans promoter::GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. All of the strains in the expression pattern database are displayed in the browse page. The records are organized by gene; information such as locus name, genomic location (WormBase), the presence of images and videos, and the actual expression pattern are shown in a tabular format. Sponsors: The Genome BC C. elegans Gene Expression Consortium is funded by Genome Canada and Genome British Columbia.

Proper citation: Expression Patterns for C. elegans promoter: GFP fusions (RRID:SCR_008354) Copy   

•   Source: SciCrunch Registry

http://abgent.com

Antibody supplier.

Proper citation: Abgent (RRID:SCR_008393) Copy   

•   Source: SciCrunch Registry

http://www.nature.com/nature/supplements/collections/

This website provides summary collections written for a broad audience highlighting some of the significant advances in a particular field. These are not scientific articles although they may reference scientific work. Sponsors: This resource is supported by Nature.com

Proper citation: Nature Supplements: Collections archive (RRID:SCR_008337) Copy   

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http://www.flexgen.nl/

A biotechnology company that has developed technology for synthesizing custom microarrays, the FlexArrayer. Its is a desk-top sized instrument which allows the researcher to generate, in their own laboratory, either a custom oligonucleotide array in a single day or oligonucleotide pool in a few days. Recent developments in synthesis chemistry allows many modifications to be incorporated or for alternative chemistries to be considered., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FlexGen (RRID:SCR_003902) Copy   

•   Source: SciCrunch Registry

http://clinicaltrials.gov/show/NCT01211678

A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise.

Proper citation: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations (RRID:SCR_004019) Copy   

•   Source: SciCrunch Registry

http://sing.ei.uvigo.es/GC/

Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.

Proper citation: GeneCommittee (RRID:SCR_004168) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hlaseq/

An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.

Proper citation: HLASeq (RRID:SCR_004185) Copy   

•   Source: SciCrunch Registry