Park Young-Kyu, Bang Ok Sun, Cha Min-Ho, Kim Jaeheup, Cole John W, Lee Doheon, Kim Young Joo
Medical Genome Research Center, KRIBB, Daejeon 305-806, Korea.
BMC Syst Biol. 2011;5 Suppl 2(Suppl 2):S10. doi: 10.1186/1752-0509-5-S2-S10. Epub 2011 Dec 14.
To understand how stroke risk factors mechanistically contribute to stroke, the genetic components regulating each risk factor need to be integrated and evaluated with respect to biological function and through pathway-based algorithms. This resource will provide information to researchers studying the molecular and genetic causes of stroke in terms of genomic variants, genes, and pathways.
Reported genetic variants, gene structure, phenotypes, and literature information regarding stroke were collected and extracted from publicly available databases describing variants, genome, proteome, functional annotation, and disease subtypes. Stroke related candidate pathways and etiologic genes that participate significantly in risk were analyzed in terms of canonical pathways in public biological pathway databases. These efforts resulted in a relational database of genetic signals of cerebral stroke, SigCS base, which implements an effective web retrieval system.
The current version of SigCS base documents 1943 non-redundant genes with 11472 genetic variants and 165 non-redundant pathways. The web retrieval system of SigCS base consists of two principal search flows, including: 1) a gene-based variant search using gene table browsing or a keyword search, and, 2) a pathway-based variant search using pathway table browsing. SigCS base is freely accessible at http://sysbio.kribb.re.kr/sigcs.
SigCS base is an effective tool that can assist researchers in the identification of the genetic factors associated with stroke by utilizing existing literature information, selecting candidate genes and variants for experimental studies, and examining the pathways that contribute to the pathophysiological mechanisms of stroke.
为了解中风风险因素如何从机制上导致中风，需要整合调节每个风险因素的遗传成分，并根据生物学功能通过基于通路的算法进行评估。该资源将为研究中风分子和遗传原因的研究人员提供有关基因组变异、基因和通路方面的信息。
从描述变异、基因组、蛋白质组、功能注释和疾病亚型的公开可用数据库中收集并提取已报道的与中风相关的遗传变异、基因结构、表型和文献信息。在公共生物通路数据库中，根据经典通路分析了与中风相关的候选通路和在风险中显著参与的病因基因。这些工作形成了一个脑卒中介导基因信号的关系数据库SigCS base，并实现了一个有效的网络检索系统。
SigCS base的当前版本记录了1943个非冗余基因、11472个遗传变异和165条非冗余通路。SigCS base的网络检索系统由两个主要搜索流程组成，包括：1）使用基因表浏览或关键词搜索进行基于基因的变异搜索，以及2）使用通路表浏览进行基于通路的变异搜索。可通过http://sysbio.kribb.re.kr/sigcs免费访问SigCS base。
SigCS base是一个有效的工具，可帮助研究人员利用现有文献信息识别与中风相关的遗传因素，选择候选基因和变异进行实验研究，并研究导致中风病理生理机制的通路。
