![]() InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. The Planteome is a resource for common reference ontologies and applications for plant biology. ![]() WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. Reactome is a free, open-source, curated and peer-reviewed pathway database that provides intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway 3ĥ Figure 1: GO hierarchy example knowledge to support basic research, genome analysis, modeling, systems biology and education. Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database of biological systems that integrates genomic, chemical and systemic functional information in pathways. The specificity of the terms varies along the tree: from very general terms (in first levels of GO) to very specific ones. Due to the complexity of hierarchy structure (directed acyclic graph), the terms can be found in several different levels. GO describes gene products in terms of their associated biological processes, cellular components and molecular functions, terms that have a hierarchical relationship (parent-child) (Figure 1). Annotation and ontology sources The Gene Ontology (GO) project aims to capture the increasing knowledge on gene function in a controlled vocabulary applicable to all the organisms. Many ontology sources exist in order to capture biological information in a meaningful way. To obtain a license key please visit: Documentation The biological interpretation of large gene clusters derived from high-throughput experiments is a real challenge. License applications are reviewed manually and an including the license key will be sent to you as soon as the evaluation process has been completed. Note that the license terms specifically limit its use to such purposes. ClueGO is available free of charge only to academic, government, and other nonprofit institutions for noncommercial, nonprofit internal research purposes. 2Ĥ License The authors wish to make ClueGO available on a nonexclusive basis to interested parties for noncommercial internal research purposes. If this folder is removed or the content damaged, it will be recreated automatically at the next startup. Cytoscape installed: At the first startup, the ClueGOConfiguration folder containing precompiled ClueGO files and sample files will be created in the user home folder. Hard disk with at least 100 MB free (for example files). Installation System Requirements: Windows, Linux, Unix or MacOS operating system. ClueGO v2.0.0 for Cytoscape was released in 13th of December The functionality of ClueGO earlier described is valid in versions ported to Cytoscape 3. ClueGO and CluePedia should be downloaded from the Cytoscape App Store through the Cytoscape App Manager (Cytoscape menu, Apps ClueGO). Human and mouse data are included by default in the App, and more than 200 organisms are available for download. ClueGO is extended by CluePedia, that allows a detailed pathways analysis. ClueGO is a Cytoscape App that facilitates the biological interpretation of large lists of genes and proteins by selecting representative Gene Onology terms and pathways from multiple ontologies and visualizes them into functionally organized networks. Apps with specific functionality extend Cytoscape and are available at the Cytoscape App Store. 1 ClueGO Documentation Gabriela Bindea and Bernhard Mlecnik Laboratory of Integrative Cancer Immunology UMRS1138 Cordeliers Research Center, Paris, FranceĢ Contents ClueGO Cytoscape App 2 Installation 2 License 2 Documentation 3 Annotation and ontology sources ClueGO features ClueGO overview ClueGO analysis steps ClueGO analysis with one or multiple lists with markers ClueGO visualization of preselected GO terms and pathways ClueGO supported organisms ClueGO predefined selection criteria of GO terms and pathways Kappa score Statistics ClueGO automation Bibliography 18 1ģ ClueGO Cytoscape App Cytoscape is a major computational platform for the analysis and visualization of biological networks.
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