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on page 1 showing 15 out of 15 results

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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    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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    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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    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 (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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Cite this (Integrated Molecular Interaction Database, RRID:SCR_003546)

URL: http://integrativebiology.org/

Resource Type: Resource, data or information resource, database

Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database.

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    KOBAS

Cite this (KOBAS, RRID:SCR_006350)

URL: http://kobas.cbi.pku.edu.cn/

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

Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available

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Cite this (MalaCards, RRID:SCR_005817)

URL: http://malacards.org

Resource Type: Resource, data or information resource, database

An integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. The database contains 17,705 diseases, consolidated from 28 sources.

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Cite this (NCBI BioSystems Database, RRID:SCR_004690)

URL: http://www.ncbi.nlm.nih.gov/biosystems/

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

Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them.

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    SEGS

Cite this (SEGS, RRID:SCR_003554)

URL: http://kt.ijs.si/software/SEGS/

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

A web tool for descriptive analysis of microarray data. The analysis is performed by looking for descriptions of gene sets that are statistically significantly over- or under-expressed between different scenarios within the context of a genome-scale experiments (DNA microarray). Descriptions are defined by using the terms from the Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene-gene interactions found in the ENTREZ database. Gene annotations by GO and KEGG terms can also be found in the ENTREZ database. The tool provides three procedures for testing the enrichment of the gene sets (over- or under-expressed): Fisher's exact test, GSEA and PAGE, and option for combining the results of the tests. Because of the multiple-hypothesis testing nature of the problem, all the p-values are computed using the permutation testing method.

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Cite this (SynSysNet, RRID:SCR_003180)

URL: http://bioinformatics.charite.de/synsysnet/

Resource Type: Resource, data or information resource, database

A curated database for synaptic proteins that provides adequate definitions of pre- and post-synaptic proteins, proteins present in sub-domains of the synapse, e.g. the synaptic vesicle and associated proteins, lipid rafts and postsynaptic density. In addition to data that was and will be gathered from the experiments conducted within SynSys - A European expertise Network on building the synapse, they have extracted and manually curated all relevant data on these proteins from other sources and provided an ontology for these. Novel splice forms are being identified that can be matched with proteomics data. Information on proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated. Proteins or compounds can be searched and Interactive Networks can be visualized. The point Diseases present neurological diseases, to illustrate the role of SynSysNet in the medication.

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    TrED

Cite this (TrED, RRID:SCR_005869)

URL: http://www.mgc.ac.cn/TrED/

Resource Type: Resource, data analysis software, data processing software, database, software application, software resource, data or information resource

TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes.

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Cite this (WebGestalt: WEB-based GEne SeT AnaLysis Toolkit, RRID:SCR_006786)

URL: http://bioinfo.vanderbilt.edu/webgestalt/

Resource Type: Resource, software resource, software toolkit, web application

A web-based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.

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