Download
1 / 16
260 likes | 705 Views
Gene Ontology&David Bioinformatics Tools. Concept. The Gene Ontology , or GO , is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. History.
E N D
Concept • The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species
History • The Gene Ontology was originally constructed in 1998 by a consortium of researchers studying the genome of three model organisms: Drosophila melanogaster (fruit fly), Mus musculus (mouse), and Saccharomyces cerevisiae (brewers' or bakers' yeast).Many other model organism databases have joined the Gene Ontology consortium, contributing not only annotation data, but also contributing to the development of the ontologies and tools to view and apply the data. As of January 2008, GO contains over 24,500 terms applicable to a wide variety of biological organisms. There is a significant body of literature on the development and use of GO, and it has become a standard tool in the bioinformatics arsenal.
Goals • Maintain and develop its controlled vocabulary of gene and gene product attributes; • Annotate genes and gene products, and assimilate and disseminate annotation data; • Provide tools for easy access to all aspects of the data provided by the project.
GO term • The Gene Ontology project provides an ontology of defined TERM representing gene product properties
Three domains • cellular component, the parts of a cell or its extracellular environment; • molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis; • biological process, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.
Tools- AmiGO • AmiGO is a web-based application that allows users to query, browse and visualize ontologies and gene product annotation data. In addition, it also has a BLAST tool,tools allowing analysis of larger data sets, and an interface to query the GO database directly
GO Consortium • The GO Consortium is the set of biological databases and research groups actively involved in the GO project. This includes a number of model organism databases and multi-species protein databases, software development groups, and a dedicated editorial office.
DAVID (bioinformatics tool) • DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB).
What David do? • All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies
Functionality Highlights • 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. • and more
Exercise • 熟悉GO数据库以及AmiGO检索方法 • 熟悉David Bioinformatics 功能分析及ID转换的使用方法 • 第3次课本地blast练习用的ID进行DAVID GO功能聚类分析，并作简单说明
