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on page 1 showing 20 out of 95 results from 1 sources

    Ancora

Cite this (Ancora, RRID:SCR_001623)

URL: http://ancora.genereg.net/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.

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    APPRIS

Cite this (APPRIS, RRID:SCR_012019)

URL: http://appris.bioinfo.cnio.es/

Resource Type: Resource, data or information resource, database

A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript.

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    ARNIE

Cite this (ARNIE, RRID:SCR_000514)

URL: http://www.sanger.ac.uk/cgi-bin/teams/team30/arnie

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

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Cite this (Bgee: a dataBase for Gene Expression Evolution, RRID:SCR_002028)

URL: http://bgee.org/

Resource Type: Resource, data or information resource, database

Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently RNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species.

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Cite this (BioGPS: The Gene Portal Hub, RRID:SCR_006433)

URL: http://biogps.org/

Resource Type: Resource, data or information resource, database

An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database.

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Cite this (BodyMap-Xs, RRID:SCR_001147)

URL: http://bodymap.genes.nig.ac.jp/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008

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Cite this (Boston Children's Hospital Center of Excellence in Molecular Hematology, RRID:SCR_015348)

URL: http://zfrhmaps.tch.harvard.edu/cemh/

Resource Type: Resource, disease-related portal, topical portal, service resource, portal, access service resource, data or information resource

Research center investigating molecular hematology through mouse and zebrafish models.

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Cite this (Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core, RRID:SCR_015352)

URL: http://zfrhmaps.tch.harvard.edu/cemh/CoreC.htm

Resource Type: Resource, service resource, core facility, access service resource

Core facility for basic and translational stem cell research. The core's areas of expertise include human pluripotent stem cell biology, cGMP cell manufacturing, reprogramming, genome editing, genotyping, laboratory automation, chemical screening, and imaging/image analysis.

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Cite this (Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core, RRID:SCR_015355)

URL: http://zfrhmaps.tch.harvard.edu/cemh/CoreB.htm

Resource Type: Resource, service resource, core facility, access service resource

Zebrafish core facility which generates and maintains transgenic and mutant fish lines for hematology research. It also provides expertise and training in model production, study design, and fish production for research.

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Cite this (Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays, RRID:SCR_001697)

URL: http://cshprotocols.cshlp.org/cgi/collection/behavioral_assays

Resource Type: Resource, bibliography, data or information resource

A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.

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Cite this (Comparative Toxicogenomics Database, RRID:SCR_006530)

URL: http://ctdbase.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.

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    CRCView

Cite this (CRCView, RRID:SCR_007092)

URL: http://crcview.hegroup.org/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.

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    CreZoo

Cite this (CreZoo, RRID:SCR_008919)

URL: http://crezoo.crt-dresden.de/crezoo/

Resource Type: Resource, organism supplier, database, biomaterial supply resource, data set, cell repository, material resource, data or information resource

Database of helpful set of CreERT2 driver lines expressing in various regions of the developing and adult zebrafish. The lines have been generated via the insertion of a mCherry-T2A-CreERT2 in a gene trap approach or by using promoter fragments driving CreERT2. You can search the list of all transgenic lines or single entries by insertions (gene) or expression patterns (anatomy/region). In most cases the CreERT2 expression profile using in situ hybridization at 24 hpf and 48 hpf is shown, but also additional information (e.g. mCherry or CreERT2 expression at adult stages, transactivation of a Cre-dependent reporter line) is displayed. Currently, not all insertions have been mapped to a genomic location but the database will be regularly updated adding newly generated insertions and mapping information. Your help in improving and broadening the database by giving your opinion or knowledge of expression patterns is highly appreciated.

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Cite this (CWRU In Vivo Animal Facilities, RRID:SCR_014209)

URL: http://corefacilities.case.edu/animal.php

Resource Type: Resource, service resource, core facility, access service resource

A set of core facilities of Case Western Reserve University School of Medicine which allows users to create and analyze in vivo animal models. The various facilities provide animal care, transgenic models, imaging, irradiation, and phenotyping for research concerning such topics as cancer, metabolic processes, and behavior. In vivo animals provided include mice, zebrafish, and rodents.

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Cite this (Disease Genes Conserved Sequence Tags Database, RRID:SCR_000760)

URL: http://dgcst.ceinge.unina.it/

Resource Type: Resource, data or information resource, database

A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions.

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Cite this (Duke O'Brien Center for Kidney Research Animal Models Core, RRID:SCR_015267)

URL: http://www.dukekidneycenter.org/cores/animal-models-core

Resource Type: Resource, service resource, core facility, access service resource

Core facility that provides access to a range of experimental models of kidney, heart and vascular diseases. It also provides comprehensive phenotyping services for kidney functions, blood pressure and other cardiovascular functions.

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Cite this (ECgene: Gene Modeling with Alternative Splicing, RRID:SCR_007634)

URL: http://genome.ewha.ac.kr/ECgene/

Resource Type: Resource, data or information resource, database

Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.

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Cite this (Edwards Lab, RRID:SCR_008860)

URL: http://edwardslab.bmcb.georgetown.edu/

Resource Type: Resource, topical portal, portal, laboratory portal, organization portal, data or information resource

The Edwards lab conducts research in various aspects of computational biology and bioinformatics, particularly proteomics and mass spectrometry informatics and DNA and protein based signatures for pathogen detection. Some tools provided by Edwards Lab are the PepArML Meta-Search Engine, PeptideMapper Web-Service, Peptide Sequence Databases, Rapid Microorganism Identification Database (RMIDb), and GlycoPeptideSearch. Our primary area of research is the analysis of mass spectrometry experiments for proteomics. Proteomics, the qualitative and quantitative analysis of the expressed proteins of a cell, makes it possible to detect and compare the protein abundance profiles of different samples. Proteins observed to be under or over expressed in disease samples can lead to diagnostic markers or drug targets. The observation of mutated or alternatively spliced protein isoforms may provide domain experts with clues to the mechanisms by which a disease operates. The detection of proteins by mass spectrometry can even signal the presence of airborne microorganisms, such as anthrax, in the detect-to-protect time-frame. Recent research has focused on the discovery of novel peptides in proteomics datasets, improving the sensitivity and specificity of peptide identification using spectral matching with hidden Markov models, and unsupervised machine-learning based peptide identification result combining. Outside of proteomics, we work on computational tools for the design of highly specific oligonucleotides useful for pathogen signatures and PCR assay design. Recent research has focused on precomputing all human oligos of length 20 that are unique up to 4 string edits; and all bacterial 20-mer oligos that are species specific up to 4 string edits.

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Cite this (EGAN: Exploratory Gene Association Networks, RRID:SCR_008856)

URL: http://akt.ucsf.edu/EGAN/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible

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Cite this (EID: Exon-Intron Database, RRID:SCR_002469)

URL: http://bpg.utoledo.edu/~afedorov/lab/eid.html

Resource Type: Resource, data set, data or information resource

Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.

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