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http://www.columbia.edu/cu/biology/faculty/yuste/
Laboratory that aims to understand the function of the cortical microcircuit by reverse-engineering of the cortical microcircuit using the mouse neocortex in vitro and in vivo as their experimental preparations. The techniques applied are electrophysiology, anatomy, and a variety of optical methods, including infrared-DIC, voltage- and ion-sensitive dye imaging with confocal, two-photon and second harmonic microscopy. They also use laser uncaging, biolistics, electroporation, electron microscopy and numerical simulations, and make extensive use of genetically modified mouse strains. They focus is on two major questions: (1) What is the function of dendritic spines? (2) What are the multicellular patterns of activity under spontaneous or evoked activation of the circuit? Resources include: * Cell Reconstructions: Cell Database, PDF Images, .DAT Files * Circuit Diagrams: Full Circuit Diagram, Inhibitory Circuit Diagram, Excitatory Circuit Diagram, Simplified Circuit Diagram, Layer to Layer Simplified Circuit, Circuit diagram references
Proper citation: Rafael Yustes Laboratory (RRID:SCR_001845) Copy
Service and training support for academic, government, and private sector scientists worldwide in genomics, including laboratory experimentation, statistical analysis, and comprehensive bioinformatics support, including large-scale genome comparisons, algorithm and tools development, and database curation, annotation and hosting. The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects: *Autism Chromosome Rearrangement Database *Cystic Fibrosis Mutation Database *The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database *Database of Genomic Variants *The Chromosome 7 Annotation Project *Human Genome Segmental Duplication Database *Non-Human Segmental Duplication Database Healthy control DNA samples from the Ontario Population Genomics Platform are available. The Biobanking and Databasing Facility provides DNA extraction from lymphoblasts, fibroblasts and other cell types, archiving of white cell pellets, preparation and immortalization of cell lines, and comprehensive databasing and tracking of samples and/or cell lines within the facility.
Proper citation: TCAG (RRID:SCR_001840) Copy
A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.
Proper citation: PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) Copy
https://gene.sfari.org/database/human-gene/
Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD. New gene submissions are welcome. Modules: * Human Gene: thoroughly annotated list of genes that have been studied in the context of autism, with information on the genes themselves, relevant references from the literature, and the nature of the evidence. Uniquely, SFARI Gene incorporates information on both common and rare variants. * Animal Model: information about lines of genetically modified mice that represent potential models of autism. This information includes the nature of the targeting construct, the background strain and, most importantly, a thorough summary of the phenotypic features of the mice that are most relevant to autism. * Protein Interaction (PIN): compilation of all known direct protein interactions for those gene products implicated in autism. It presents both graphical and tabular views of interactomes, highlighting connections between autism candidate genes. Each protein interaction is manually verified by consultation with the primary reference. * Copy Number Variant (CNV): a parallel resource providing genetic information about all known copy number variants linked to autism. * Gene Scoring: includes a "score" for each autism candidate gene, based on an assessment of the strength of human genetic evidence.
Proper citation: AutDB (RRID:SCR_001872) Copy
http://datahub.io/dataset/kupkb
A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made.
Proper citation: Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Time-series data sets spanning twelve time-points between E12-P9 for exploring cerebellar development of the mouse in time and space. The database contains a number of mutant / wildtype microarray datasets including two complete wildtype microarray time-series (C57BL/6 and DBA/2J). The dataset also includes in situ hybridization and bioinformatic analyses. Exploration of this dataset will allow the investigator to assess differential gene expression profiles from a developing mutant cerebella, to assess the temporal changes in gene expression in the wildtype, and to verify the cellular expression of these genes in images from our in situ hybridization library. Using the database, the investigator can explore the developmental expression or differential expression patterns of a particular gene, or create lists of similarly expression genes by building simple search algorithms. These lists can then be mined across all the datasets in both space and time. Cb GRiTS's current datasets represent gene expression analyses from multiple cerebellar mutant and wildtype single time-point and developmental series.
Proper citation: Cerebellar Gene Regulation in Time and Space Database (RRID:SCR_001699) Copy
A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database.
Proper citation: MouseCyc (RRID:SCR_001791) Copy
http://neuromorpho.org/index.jsp
Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.
Proper citation: NeuroMorpho.Org (RRID:SCR_002145) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.
Proper citation: Cell Centered Database (RRID:SCR_002168) Copy
http://biodev.extra.cea.fr/interoporc/
Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.
Proper citation: InteroPorc (RRID:SCR_002067) Copy
A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
Proper citation: PROVEAN (RRID:SCR_002182) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. They have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells, and papers. The community can contribute to this resource.
Proper citation: CistromeMap (RRID:SCR_002173) Copy
http://tvmouse.compmed.ucdavis.edu/
Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.
Proper citation: Visible Mouse Project (RRID:SCR_002393) Copy
Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
Proper citation: Ensembl (RRID:SCR_002344) Copy
http://www.ncbi.nlm.nih.gov/SNP/
Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.
Proper citation: dbSNP (RRID:SCR_002338) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Project mapping whole mouse brain connectivity using serial block face scanning electron microscopy (SBF-SEM) with a specially-designed whole-brain microtome (WBM). With any luck, the whole mouse brain will be mapped ultrastructurally in the near term, which will then open the door to more serious problems; reliable automated segmentation and circuit reconstruction. These will undoubtedly require advances in machine learning methods and their application. Connectomics Software and a Multiresolution Image Viewer (MIV) is also available.
Proper citation: Connectomes.org (RRID:SCR_002243) Copy
https://www.genevestigator.com/gv/
A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.
Proper citation: Genevestigator (RRID:SCR_002358) Copy
The e-mouse.org is an online resource that aims to bring together and provide users with all information related to the laboratory mouse and its use as a model organism. Users can find direct links to MRB, a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, as well as the CreZOO, MMdb and Fleming Databases, three more specialized mouse repositories, all developed and hosted at the B.S.R.C. Alexander Fleming Institute. Additionally e-mouse.org provides links to major European and international mouse resources like the Mouse Genome Informatics (MGI), European Mouse Mutant Archive (EMMA), International Mouse Strain Resource (IMSR) and Ensembl. Users interested in retrieving information regarding the use of mouse models are encouraged to visit MRB which provides an index of publicly available mouse resources intended for both bench scientists and bioinformaticians. * Mouse Resource Browser (MRB) is a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, classified in 22 categories. * CreZOO is the European virtual repository of Cre and other targeted conditional driver strains. Its aim is to capture and disseminate extant and new information on all Cre driver strains. * MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. * Fleming Database is a fully searchable resource developed to host all mouse strains developed and/or housed in BSRC Al. Fleming's animal house. * MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. * EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. * IMSR is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant, and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research. * Ensembl is a project that produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
Proper citation: e-mouse.org (RRID:SCR_000623) Copy
http://www.knockoutmouse.org/about/eucommtools
Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE.
Proper citation: EUCOMMTOOLS (RRID:SCR_000676) Copy
http://eumorphia.publicwebserver3.har.mrc.ac.uk/
A portal documenting a project for the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. EUMORPHIA has developed a new robust primary screening platform for determining the phenotype of mice: EMPReSS - European Mouse Phenotyping Resource for Standardised Screens. The project is also focused on training new young scientists by funding them to work in a variety of laboratories to gain a broader swathe of techniques. The project has also identified the need for more trained mouse pathologists. To address this, they are setting up training courses in pathology and working at a European level to establish more training.
Proper citation: Understanding Human Disease Through Mouse Genetics (RRID:SCR_000785) Copy
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