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on page 1 showing 20 out of 35 results from 1 sources

    aGEM

Cite this (aGEM, RRID:SCR_013349)

URL: http://agem.cnb.csic.es/VisualOmics/aGEM/

Resource Type: Resource, data or information resource, database

Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display.

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Cite this (Algal Functional Annotation Tool, RRID:SCR_012034)

URL: http://pathways.mcdb.ucla.edu/algal/

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

Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.

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Cite this (Allen Institute Neurowiki, RRID:SCR_005042)

URL: http://neurowiki.alleninstitute.org/index.php/Main_Page

Resource Type: Resource, wiki, data or information resource, database, narrative resource, ontology, controlled vocabulary

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. The Allen Institute Neurowiki is a joint project between Vulcan Inc. and the Allen Institute to build a Semantic Wiki mapping genetic instances. It is a finished prototype testing the import pipelines and display componenets for combining 5 major RDF datasets from 4 different sources. Current planning includes mapping complete datasets, curating a better ontology, and creating multiple ontology management for a user class. Biological Linked Data Map: * Open, public online access * Data from multiple RDF data stores * Complete import pipeline using LDIF framework * Outlines of each imported instance embedding inline wiki properties and providing views of imported properties from original RDF datasets * Charting tools that ''''pivot'''' SPARQL queries providing several views of each query * Navigation and composition tools for accessing and mining the data Where did we get the data? * KEGG: Kyoto Encyclopedia of Genes and Genomes: KEGG GENES is a collection of gene catalogs for all complete genomes generated from publicly available resources, mostly NCBI RefSeq * Diseasome: The Diseasome website is a disease / disorder relationships explorer and a sample of an innovative map-oriented scientific work. Built by a team of researchers and engineers, it uses the Human Disease Network dataset. * DrugBank: The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. * Sider: Sider contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. Every piece of content on every instance page is generated by Semantic Result Formatters interpreting SPARQL results.

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Cite this (Babelomics, RRID:SCR_002969)

URL: http://babelomics.bioinfo.cipf.es

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

An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool

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Cite this (BioExtract, RRID:SCR_005397)

URL: http://www.bioextract.org/GuestLogin

Resource Type: Resource, service resource

An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.

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    ClueGO

Cite this (ClueGO, RRID:SCR_005748)

URL: http://www.ici.upmc.fr/cluego/

Resource Type: Resource, software resource

A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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Cite this (ConsensusPathDB, RRID:SCR_002231)

URL: http://cpdb.molgen.mpg.de

Resource Type: Resource, data or information resource, database

An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.

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Cite this (Cotton EST Database, RRID:SCR_003301)

URL: http://www.leonxie.com/

Resource Type: Resource, data or information resource, database

Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information.

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    DAVID

Cite this (DAVID, RRID:SCR_001881)

URL: http://david.abcc.ncifcrf.gov/

Resource Type: Resource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, service resource, software resource, data or information resource

An integrated biological knowledgebase and comprehensive set of functional annotation tools for investigators to understand biological meaning behind large lists of genes. For any given gene list, DAVID tools are able to: - Identify enriched biological themes, particularly GO terms - Discover enriched functional-related gene groups - Cluster redundant annotation terms - Visualize genes on BioCarta & KEGG pathway maps - Display related many-genes-to-many-terms on 2-D view. - Search for other functionally related genes not in the list - List interacting proteins - Explore gene names in batch - Link gene-disease associations - Highlight protein functional domains and motifs - Redirect to related literatures - Convert gene identifiers from one type to another.

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    ENZYME

Cite this (ENZYME, RRID:SCR_002487)

URL: http://www.expasy.org/enzyme/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. These include * EC number * Recommended name * Alternative names (if any) * Catalytic activity * Cofactors (if any) * Pointers to the Swiss-Prot protein sequence entry(ies) that correspond to the enzyme (if any) * Pointers to human disease(s) associated with a deficiency of the enzyme (if any) We believe that the ENZYME database can be useful to anybody working with enzymes and that it can be of help in the development of computer programs involved with the manipulation of metabolic pathways. Available services include downloading ENZYME by FTP as well as report forms for a new ENZYME entry or for an error/update in an existing entry.

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Cite this (eQuilibrator, RRID:SCR_006011)

URL: http://equilibrator.weizmann.ac.il/

Resource Type: Resource, software resource, database, data or information resource, web application

Web interface designed for thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions. It can provide estimates for compounds in the KEGG database, and individual compounds and enzymes can be searched for by their common names (water, glucosamine, hexokinase). Reactions can be entered in a free-text format that eQuilibrator parses automatically. eQuilibrator also allows manipulation of the conditions of a reaction - pH, ionic strength, and reactant and product concentrations.

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Cite this (ExplorEnz, RRID:SCR_002665)

URL: http://www.enzyme-database.org

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Enzyme database developed as a way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards. A simple, easy to use, web-based query interface is provided (Search), along with an advanced search engine for more complex queries (Advanced Search). Forms are provided to submit suggestions for new enzyme entries or to report errors in existing entries. Downloads of the database are available via FTP as SQL or XML.

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    FlyMine

Cite this (FlyMine, RRID:SCR_002694)

URL: http://www.flymine.org/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resource

An integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

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Cite this (FunNet - Transcriptional Networks Analysis, RRID:SCR_006968)

URL: http://www.funnet.info/

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

Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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    FunTree

Cite this (FunTree, RRID:SCR_006014)

URL: http://www.ebi.ac.uk/thornton-srv/databases/FunTree/

Resource Type: Resource, data or information resource, database

FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms.

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Cite this (GeneCodis, RRID:SCR_006943)

URL: http://genecodis.cnb.csic.es/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology.

  • From Current Category

Cite this (GeneTerm Linker, RRID:SCR_006385)

URL: http://gtlinker.cnb.csic.es/

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

Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service.

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Cite this (GeneTrail, RRID:SCR_006250)

URL: http://genetrail.bioinf.uni-sb.de/

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

A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes.

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Cite this (hiPathDB - human integrated Pathway DB with facile visualization, RRID:SCR_008900)

URL: http://hipathdb.kobic.re.kr/

Resource Type: Resource, data or information resource, database

hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. (2010.03.09) hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways.

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    INMEX

Cite this (INMEX, RRID:SCR_004173)

URL: http://www.inmex.ca./INMEX/

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

A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner.

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