LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.
LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.
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DOI：
10.1186/s12920-018-0351-0
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发表时间：
2018-04-20
影响因子：
2.7
通讯作者：
Zheng J
中科院分区：
文献类型：
--
作者：
Guo J;Chen H;Yang P;Lee YT;Wu M;Przytycka TM;Kwoh CK;Zheng J
减数分裂重组发生在减数分裂过程中，从双亲继承的染色体交换遗传物质，在配子细胞中产生染色体。重组事件往往发生在称为重组热点的狭窄基因组区域。它的失调可能会导致严重的人类疾病，如出生缺陷。虽然重组事件的调控机制尚不清楚，但DNA序列多态已被发现在重组热点的调控中起着关键作用。为了便于对其内在机制的研究，我们开发了一个名为LDSplitDB的数据库，该数据库为重组热点的全基因组关联研究提供了一个集成的、交互式的数据挖掘和可视化平台。它包含1000基因组计划和HapMap第三阶段数据集中主要组织相容性复合体(MHC)区域的预先计算的关联图，以及来自HapMap第二阶段数据集的欧洲人口基因组规模研究。除了重组谱外，还提供了可能与减数分裂重组相关的基因、SNPs和不同类型的表观遗传修饰的相关数据，以供综合分析。为了满足快速增长的群体基因组学数据的计算需求，我们使用著名的LDhat算法准备了一个包含400个单倍型的查找表，用于重组率估计，其中包括所有可能的两个座位单倍型配置。据我们所知，LDSplitDB是第一个用于人类重组热点与DNA序列多态性关联分析的大型数据库。这为发现减数分裂重组热点的机制提供了宝贵的资源。该数据库中有关MHC的信息有助于理解重组在人类免疫系统中的作用。Http://histone.scse.ntu.edu.sg/LDSplitDB
Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. http://histone.scse.ntu.edu.sg/LDSplitDB
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影响因子：
4.5
作者：
Liu S;Yeh CT;Ji T;Ying K;Wu H;Tang HM;Fu Y;Nettleton D;Schnable PS
通讯作者：
Schnable PS
影响因子：
30.8
作者：
Jeffreys, AJ;Neumann, R
通讯作者：
Neumann, R
影响因子：
5.3
作者：
Getun, Irina V.;Wu, Zhen;Bois, Philippe R. J.
通讯作者：
Bois, Philippe R. J.
影响因子：
3.8
作者：
Lam, T. H.;Shen, M.;Ren, E. C.
通讯作者：
Ren, E. C.
DOI：
10.1073/pnas.86.23.9389
发表时间：
1989-12-01
影响因子：
11.1
作者：
CUI, XF;LI, HH;ARNHEIM, N
通讯作者：
ARNHEIM, N