SNP@Evolution: a hierarchical database of positive selection on the human genome.
SNP@Evolution: a hierarchical database of positive selection on the human genome.
复制标题
SNP@Evolution：人类基因组正选择的分层数据库
DOI：
10.1186/1471-2148-9-221
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发表时间：
2009-09-05
影响因子：
3.4
通讯作者：
Zeng C
中科院分区：
文献类型：
--
作者：
Cheng F;Chen W;Richards E;Deng L;Zeng C
背景
积极选择是塑造现代人类的驱动力。高通量技术和相应统计工具的最新发展使得在人群规模上进行全基因组调查以及各种测量成为可能，例如杂合性（HET）、F
英石
和 Tajima 的 D 已应用于多个数据集来识别正选择信号。然而，需要付出巨大的努力来整合来自各个来源的各种类型的数据，并且数据集之间的不兼容是一个常见问题。 SNP@Evolution是一个集成了多个数据集的新数据库，将极大地协助该领域的未来工作。
描述
作为我们对 HapMap 第二阶段和第三阶段数据集中的进化信号进行研究扫描的一部分，我们将 SNP@Evolution 构建为专注于正选择的多方面数据库。 SNP@Evolution 拥有众多功能，其中包括计算 F
英石
所有 HapMap SNP 的 HET、每个合格基因 5 个以上 HapMap SNP，以及通过全基因组窗口扫描检测到的所有常染色体区域。为了尝试捕获整个基因组中的多个选择信号，HET、F 的选择信号富集强度 (ES) 值
英石
，并且大多数注释基因的 iHS P 值已计算并集成在一个框架内，供用户搜索异常值。具有显着 ES 或 P 值（阈值分别为 0.95 和 0.05）的基因已用颜色突出显示。通过以 10 kb 步长滑动 100 kb 窗口，可以检测到低多样性染色体区域。为了使这些信息能够轻松传播，我们使用通用模型生物数据库工具包构建了图形用户界面（GBrowser）。
结论
SNP@Evolution 是一个专注于人类基因组正向选择的分层数据库，网址为 http://bighapmap.big.ac.cn。基于 HapMap II 期和 III 期数据，SNP@Evolution 包括 3,619,226/1,389,498 个 SNP 及其计算的 HET 和 F
英石
，以及ES值为HET和F的合格基因21,859/21,099
英石
。在至少一个 HapMap 群体中，选择信号的窗口扫描产生了 1,606/10,138 个大的低 HET 区域。在第二期和第三期地域组中，660和464个地区表现出较强的分化。
Background
Positive selection is a driving force that has shaped the modern human. Recent developments in high throughput technologies and corresponding statistics tools have made it possible to conduct whole genome surveys at a population scale, and a variety of measurements, such as heterozygosity (HET), F
ST
, and Tajima's D, have been applied to multiple datasets to identify signals of positive selection. However, great effort has been required to combine various types of data from individual sources, and incompatibility among datasets has been a common problem. SNP@Evolution, a new database which integrates multiple datasets, will greatly assist future work in this area.
Description
As part of our research scanning for evolutionary signals in HapMap Phase II and Phase III datasets, we built SNP@Evolution as a multi-aspect database focused on positive selection. Among its many features, SNP@Evolution provides computed F
ST
and HET of all HapMap SNPs, 5+ HapMap SNPs per qualified gene, and all autosome regions detected from whole genome window scanning. In an attempt to capture multiple selection signals across the genome, selection-signal enrichment strength (ES) values of HET, F
ST
, and P-values of iHS of most annotated genes have been calculated and integrated within one frame for users to search for outliers. Genes with significant ES or P-values (with thresholds of 0.95 and 0.05, respectively) have been highlighted in color. Low diversity chromosome regions have been detected by sliding a 100 kb window in a 10 kb step. To allow this information to be easily disseminated, a graphical user interface (GBrowser) was constructed with the Generic Model Organism Database toolkit.
Conclusion
Available at http://bighapmap.big.ac.cn, SNP@Evolution is a hierarchical database focused on positive selection of the human genome. Based on HapMap Phase II and III data, SNP@Evolution includes 3,619,226/1,389,498 SNPs with their computed HET and F
ST
, as well as qualified genes of 21,859/21,099 with ES values of HET and F
ST
. In at least one HapMap population group, window scanning for selection signals has resulted in 1,606/10,138 large low HET regions. Among Phase II and III geographical groups, 660 and 464 regions show strong differentiation.
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影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
7
作者：
Pickrell, Joseph K.;Coop, Graham;Pritchard, Jonathan K.
通讯作者：
Pritchard, Jonathan K.
影响因子：
9.8
作者：
Rakyan, VK;Hildmann, T;Beck, S
通讯作者：
Beck, S
影响因子：
30.8
作者：
Iafrate, AJ;Feuk, L;Lee, C
通讯作者：
Lee, C
影响因子：
9.8
作者：
Bersaglieri, T;Sabeti, PC;Hirschhorn, JN
通讯作者：
Hirschhorn, JN