KOBAS server: a web-based platform for automated annotation and pathway   identification

doi:10.1093/nar/gkl167

CORC > 北京大学 > 生命科学学院

	KOBAS server: a web-based platform for automated annotation and pathway identification
	Wu, Jianmin ; Mao, Xizeng ; Cai, Tao ; Luo, Jingchu ; Wei, Liping
刊名	核酸研究
	2006
关键词	GENE-EXPRESSION DATA ALZHEIMER-DISEASE ONTOLOGY TOOL KEGG GENOMES
DOI	10.1093/nar/gkl167
英文摘要	There is an increasing need to automatically annotate a set of genes or proteins ( from genome sequencing, DNA microarray analysis or protein 2D gel experiments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously demonstrated the KEGG Orthology ( KO) as an effective alternative controlled vocabulary and developed a standalone KO- Based Annotation System ( KOBAS). Here we report a KOBAS server with a friendly web-based user interface and enhanced functionalities. The server can support input by nucleotide or amino acid sequences or by sequence identifiers in popular databasesand can annotate the input withKO terms and KEGG pathways by BLAST sequence similarity or directly ID mapping to genes with known annotations. The server can then identify both frequent and statistically enriched pathways, offering the choices of four statistical tests and the option of multiple testing correction. The server also has a 'User Space' in which frequent users may store and manage their data and results online. We demonstrate the usability of the server by finding statistically enriched pathways in a set of upregulated genes in Alzheimer's Disease ( AD) hippocampal cornu ammonis 1 ( CA1). KOBAS server can be accessed at http://kobas.cbi.pku.edu.cn.; http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000245650200145&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701 ; Biochemistry & Molecular Biology; SCI(E); PubMed; 134; ARTICLE; ,SI; W720-W724; 34
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/345780]
专题	生命科学学院
推荐引用方式 GB/T 7714	Wu, Jianmin,Mao, Xizeng,Cai, Tao,et al. KOBAS server: a web-based platform for automated annotation and pathway identification[J]. 核酸研究,2006.
APA	Wu, Jianmin,Mao, Xizeng,Cai, Tao,Luo, Jingchu,&Wei, Liping.(2006).KOBAS server: a web-based platform for automated annotation and pathway identification.核酸研究.
MLA	Wu, Jianmin,et al."KOBAS server: a web-based platform for automated annotation and pathway identification".核酸研究 (2006).