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http://caintegrator-info.nci.nih.gov/rembrandt

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Repository of molecular brain neoplasia data (RRID:SCR_004704) Copy   

•   Source: SciCrunch Registry

http://www.pantherdb.org/

System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PANTHER (RRID:SCR_004869) Copy   

•   Source: SciCrunch Registry

http://isaac.bioapps.biozentrum.uni-wuerzburg.de/isaac/modules/genome/species.xhtml

Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups.

Proper citation: InterSpecies Analysing Application using Containers (RRID:SCR_006243) Copy   

•   Source: SciCrunch Registry

http://www.conceptwiki.org

A community owned repository of concepts used to define all concepts unambiguously. Users can edit and add their own concepts to the wiki.

Proper citation: ConceptWiki (RRID:SCR_006362) Copy   

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http://bioinformatics.ubc.ca/ermineJ/

Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: ErmineJ (RRID:SCR_006450) Copy   

•   Source: SciCrunch Registry

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   

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http://flybase.org/

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

Proper citation: FlyBase (RRID:SCR_006549) Copy   

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http://www.ebi.ac.uk/Rebholz-srv/ebimed/

A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading.

Proper citation: EBIMed (RRID:SCR_005314) Copy   

•   Source: SciCrunch Registry

http://www.coremine.com/medical/#search

Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles.

Proper citation: Coremine Medical (RRID:SCR_005323) Copy   

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http://cgap.nci.nih.gov/Genes/GOBrowser

With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool

Proper citation: CGAP GO Browser (RRID:SCR_005676) Copy   

•   Source: SciCrunch Registry

http://vortex.cs.wayne.edu/projects.htm#Onto-Express

The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool

Proper citation: Onto-Express (RRID:SCR_005670) Copy   

•   Source: SciCrunch Registry

http://www.genetools.us

Web-service providing access to database that brings together information from broad range of resources. Web application for functional annotation and statistical hypothesis testing. Provides tools for analysis of genomic and microarray data. Collection of tools include Bibliographic Information,Databases,Gene Annotation,Gene Regulation, Microarray,Proteins,Sequence Manipulation - Nucleic Acids,Sequence Manipulation - Protein, Systems Biology.

Proper citation: GeneTools (RRID:SCR_005663) Copy   

•   Source: SciCrunch Registry

http://search.cpan.org/~cmungall/go-perl/

go-perl is a set of Perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for the OBO and GO gene association file formats. It has a graph-based object model with methods for graph traversal. For more details, see the documentation included with the modules. go-perl comes bundled with XSL (Extensible Stylesheet Language) transforms (which can also be used independently of Perl, provided you have files in OBO-XML format), as well as scripts that can be used as standalone tools. Installation should be simple, provided you have some experience with Perl and CPAN; see the INSTALL file for details. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: go-perl (RRID:SCR_005730) Copy   

•   Source: SciCrunch Registry

http://search.cpan.org/~cmungall/go-db-perl/

Software resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: go-db-perl (RRID:SCR_005721) Copy   

•   Source: SciCrunch Registry

http://manatee.sourceforge.net/

Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris

Proper citation: Manatee (RRID:SCR_005685) Copy   

•   Source: SciCrunch Registry

http://genenet2.uthsc.edu/geneinfoviz/search.php

GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool

Proper citation: GeneInfoViz (RRID:SCR_005680) Copy   

•   Source: SciCrunch Registry

http://basalganglia.huji.ac.il/links.htm

GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GOdist (RRID:SCR_005770) Copy   

•   Source: SciCrunch Registry

http://compbio.charite.de/contao/index.php/ontologizer2.html

The Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods. The tool can be started directly from the web using Java webstart. For graph visualizations, users need to install the GraphViz library. The tool is freely available to all, and source code is available at SourceForge. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Ontologizer (RRID:SCR_005801) Copy   

•   Source: SciCrunch Registry

http://thea.unice.fr/index-en.html

THIS RESOURCE IS NO LONGER IN SERVICE, on documented July 16, 2012. An integrated information processing system dedicated to the analysis of post-genomic data. It allows automatic annotation of data issued from classification systems with selected biological information (including the Gene Ontology). Users can either manually search and browse through these annotations, or automatically generate meaningful generalizations according to statistical criteria (data mining). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: THEA - Tools for High-throughput Experiments Analysis (RRID:SCR_005802) Copy   

•   Source: SciCrunch Registry

http://pubsearch.stanford.edu/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: PubSearch (RRID:SCR_005830) Copy   

•   Source: SciCrunch Registry