Tools   Select Another Resource Report Type

http://ctdbase.org/

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.

Proper citation: Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) Copy   

•   Source: SciCrunch Registry

http://www.ihop-net.org/UniPub/iHOP/

Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.

Proper citation: Information Hyperlinked Over Proteins (RRID:SCR_004829) Copy   

•   Source: SciCrunch Registry

http://llama.mshri.on.ca/funcassociate/

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-7/search?q=*

Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD).

Proper citation: Integrated Gene-Disease Interaction (RRID:SCR_006173) Copy   

•   Source: SciCrunch Registry

http://biogps.org/

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.

Proper citation: BioGPS: The Gene Portal Hub (RRID:SCR_006433) Copy   

•   Source: SciCrunch Registry

http://crcview.hegroup.org/

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.

Proper citation: CRCView (RRID:SCR_007092) Copy   

•   Source: SciCrunch Registry

https://omictools.com/ecgene-tool

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.

Proper citation: ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) Copy   

•   Source: SciCrunch Registry

http://www.genomicus.biologie.ens.fr/genomicus-72.01/cgi-bin/search.pl

A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Proper citation: Genomicus (RRID:SCR_011791) Copy   

•   Source: SciCrunch Registry

https://neuinfo.org/about/sources/nlx_143622-1

International registry of biomaterial supply resources both for transplantation and research. Contributions to this resource are welcome. The database is searchable through NIF and is updated regularly.

Proper citation: One Mind Biospecimen Bank Listing (RRID:SCR_004193) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/mapview/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

Proper citation: MapViewer (RRID:SCR_003092) Copy   

•   Source: SciCrunch Registry

http://www.biocomputing.it/fidea/

A web server for the functional interpretation of differential expression analysis. It can: * Calculate overrepresentation statistics using KEGG, Interpro, Gene Ontology Molecular Function, Gene Ontology Biological Process, Gene Ontology Cellular Component and GoSlim classifications; * Analyze down-regulated and up-regulated DE genes separately or together as a single set; * Provide interactive graphs and tables that can be modified on the fly according to user defined parameters; the user can set a fold change filter and interactively see the effects on the gene set under examination; * Output publication-ready plot of the graph; * Compare the results of several experiments in any combination.

Proper citation: FIDEA (RRID:SCR_004187) Copy   

•   Source: SciCrunch Registry

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

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

Proper citation: BodyMap-Xs (RRID:SCR_001147) Copy   

•   Source: SciCrunch Registry

http://www.germonline.org/

Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips).

Proper citation: GermOnline (RRID:SCR_002807) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/homologene

Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.

Proper citation: HomoloGene (RRID:SCR_002924) Copy   

•   Source: SciCrunch Registry

http://zfin.org

Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

Proper citation: Zebrafish Information Network (ZFIN) (RRID:SCR_002560) Copy   

•   Source: SciCrunch Registry

http://www.zfatlas.psu.edu/

Atlas containing 2- and 3-dimensional, anatomical reference slides of the lifespan of the zebrafish to support research and education worldwide. Hematoxylin and eosin histological slides, at various points in the lifespan of the zebrafish, have been scanned at 40x resolution and are available through a virtual slide viewer. 3D models of the organs are reconstructed from plastic tissue sections of embryo and larvae. The size of the zebrafish, which allows sections to fall conveniently within the dimensions of the common 1 x 3 glass slide, makes it possible for this anatomical atlas to become as high resolution as for any vertebrate. That resolution, together with the integration of histology and organ anatomy, will create unique opportunities for comparisons with both smaller and larger model systems that each have their own strengths in research and educational value. The atlas team is working to allow the site to function as a scaffold for collaborative research and educational activity across disciplines and model organisms. The Zebrafish Atlas was created to answer a community call for a comprehensive, web-based, anatomical and pathological atlas of the zebrafish, which has become one of the most widely used vertebrate animal models globally. The experimental strengths of zebrafish as a model system have made it useful for a wide range of investigations addressing the missions of the NIH and NSF. The Zebrafish Atlas provides reference slides for virtual microscopic viewing of the zebrafish using an Internet browser. Virtual slide technology allows the user to choose their own field of view and magnification, and to consult labeled histological sections of zebrafish. We are planning to include a complete set of embryos, larvae, juveniles, and adults from approximately 25 different ages. Future work will also include a variety of comparisons (e.g. normal vs. mutant, normal vs. diseased, multiple stages of development, zebrafish with other organisms, and different types of cancer).

Proper citation: Zebrafish Atlas (RRID:SCR_006722) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: Disease Genes Conserved Sequence Tags Database (RRID:SCR_000760) Copy   

•   Source: SciCrunch Registry

https://www.facebase.org/

A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse.

Proper citation: FaceBase (RRID:SCR_005998) Copy   

•   Source: SciCrunch Registry

http://www.oeb.harvard.edu/faculty/hartl/old_site/lab/publications/GeneMerge.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GeneMerge (RRID:SCR_005744) Copy   

•   Source: SciCrunch Registry

https://github.com/ncguilbeault/BonZeb

Open source, modular software tools for high resolution zebrafish tracking and analysis.Software suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed loop experiments.Can be used in open loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data.

Proper citation: BonZeb (RRID:SCR_021392) Copy   

•   Source: SciCrunch Registry