HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants.
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants.
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DOI：
10.1093/nar/gkr917
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发表时间：
2012-01
影响因子：
14.9
通讯作者：
Kellis M
中科院分区：
文献类型：
--
作者：
Ward LD;Kellis M
全基因组关联研究（GWAS）的分辨率受到被研究群体连锁不平衡（LD）结构的限制。在编码序列中选择LD块中最可能的因果变异相对简单，但当所有变异都是基因间的时候就比较困难了。近年来，保护信息和表观基因组信息的可用性促进了对功能性非编码序列的预测。我们提出了HaploReg，一个在已发表的GWAS或新变体集的结果中探索非编码基因组注释的工具。利用来自1000基因组计划的LD信息，可以可视化链接的snp和小索引，以及它们在9种细胞类型中的预测染色质状态，哺乳动物的保守性及其对调控基序的影响。分析了一系列snp，例如由GWAS产生的snp，以富集细胞类型特异性增强子。HaploReg将有助于研究人员发展非编码变异对临床表型和正常变异影响的机制假设。HaploReg数据库可在http://compbio.mit.edu/HaploReg上获得。
The resolution of genome-wide association studies (GWAS) is limited by the linkage disequilibrium (LD) structure of the population being studied. Selecting the most likely causal variants within an LD block is relatively straightforward within coding sequence, but is more difficult when all variants are intergenic. Predicting functional non-coding sequence has been recently facilitated by the availability of conservation and epigenomic information. We present HaploReg, a tool for exploring annotations of the non-coding genome among the results of published GWAS or novel sets of variants. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals and their effect on regulatory motifs. Sets of SNPs, such as those resulting from GWAS, are analyzed for an enrichment of cell type-specific enhancers. HaploReg will be useful to researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. The HaploReg database is available at http://compbio.mit.edu/HaploReg.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
DOI：
10.1126/science.1162327
发表时间：
2009-06-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Badis G;Berger MF;Philippakis AA;Talukder S;Gehrke AR;Jaeger SA;Chan ET;Metzler G;Vedenko A;Chen X;Kuznetsov H;Wang CF;Coburn D;Newburger DE;Morris Q;Hughes TR;Bulyk ML
通讯作者：
Bulyk ML
影响因子：
46.9
作者：
Berger, Michael F.;Philippakis, Anthony A.;Bulyk, Martha L.
通讯作者：
Bulyk, Martha L.
影响因子：
5.8
作者：
Macintyre, Geoff;Bailey, James;Kowalczyk, Adam
通讯作者：
Kowalczyk, Adam
影响因子：
7
作者：
Ng, PC;Henikoff, S
通讯作者：
Henikoff, S