Gene Ontology Consortium And GO Database

Gene Ontology: tool for the unification of biology

M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig, M A Harris, D P Hill, L Issel-Tarver, A Kasarskis, S Lewis, J C Matese, J E Richardson, M Ringwald, G M Rubin & G Sherlock Nature Genetics 25, 25 - 29 (2000).

http://www.geneontology.orghttp://www.godatabase.orghttp://www.geneontology.org/GO.contents.doc.shtml

The Open Biomedical Ontology (OBO)

The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary (GO term) that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.

Go Database: lists of the genes or gene products associated with their particular GO terms, their links to the gene-association files for each of the collaborating databases is available.

The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in a species-independent manner with three kinds of terms:

biological processes cellular components molecular functions

An Example of Biological Processes

An Example of Molecular Functions

An Example of Cellular Components

The Tree View inAmiGo

Data Component of GO Database

http://www.geneontology.org/GO.current.annotations.shtml

How to Search Genes in GO?

Go TermsGene Symbol or NameFASTA Search

What The Search Result Includes?

Go Terms And GO IDSequence And Basic Sequence InformationOriginal Database And Detailed Annotation(Evidence)

Main Resource in GO Website

Go DatabaseOn Line QueryTools (Consortium and Non-Consortium)Documents and tutorial

Available Format of Go Database

TXT Format

XML Format

MySQL Format

GO Database Schema In MySQL

What are the possible uses of GO?

* integrating proteomic information from different organisms;

* assigning functions to protein domains;

* finding functional similarities in genes that are overexpressed or

underexpressed in diseases and as we age;

* predicting the likelihood that a particular gene is involved in diseases

that haven't yet been mapped to specific genes;

* analysing groups of genes that are co-expressed during

development;

* developing automated ways of deriving information about gene

function from the literature;

* verifying models of genetic, metabolic and product interaction

networks.

KEGG(Kyoto Encyclopedia of Genes and Genomes 京都基因与基因组百科全书 )

• KEGG(Kyoto Encyclopedia of Genes and Genomes)是系统分析基因功能、基因组信息数据库，它有助于研究者把基因及表达信息作为一个整体网络进行研究。基因组信息存储在GENES数据库里，包括完整和部分测序的基因组序列；更高级的功能信息存储在 PATHWAY数据库里，包括图解的细胞生化过程如代谢、膜转运、信号传递、细胞周期，还包括同系保守的子通路等信息； KEGG

的另一个数据库是 LIGAND，包含关于化学物质、酶分子、酶反应等信息。可以免费获取。 KEGG提供的整合代谢途径 (pathway)查询十分出色，包括碳水化合物、核苷、氨基酸等的代谢及有机物的生物降解，不仅提供了所有可能的代谢途径，而且对催化各步反应的酶进行了全面的注解，包含有氨基酸序列、 PDB库的链接等等。 KEGG是进行生物体内代谢分析、代谢网络研究的强有力工具。