dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq.
dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq.
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dbInDel：通过 H3K27ac ChIP-Seq 分析获得的增强子相关插入和删除变体数据库。
DOI：
10.1093/bioinformatics/btz770
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发表时间：
2020-03-01
期刊：
影响因子：
--
通讯作者：
Chen X
中科院分区：
文献类型：
--
作者：
Huang M;Wang Y;Yang M;Yan J;Yang H;Zhuang W;Xu Y;Koeffler HP;Lin DC;Chen X
癌症标志依赖于其特定的转录程序，这些程序受到多种机制的失调，包括DNA调控区的基因组畸变。全基因组关联研究表明，在推定的增强子元件中发现了许多变体。为了深入了解增强子相关非编码变体在癌症表观基因组中的调节作用，并促进功能性非编码突变的鉴定，我们提出了dbInDel，这是一个数据库，我们使用ChIP-Seq数据全面分析了人和鼠样本的增强子相关插入和缺失变体。此外，我们提供了识别和可视化的上游TF结合基序在含InDel增强子。下游靶基因也在癌症生物学的背景下进行预测和分析。dbInDel数据库促进了对癌症表观基因组中非编码变体的功能贡献的研究。数据库dbInDel可从http://enhancer-indel.cam-su.org/访问。 补充数据可在Bioinformatics在线获得。
Cancer hallmarks rely on its specific transcriptional programs, which are dysregulated by multiple mechanisms, including genomic aberrations in the DNA regulatory regions. Genome-wide association studies have shown many variants are found within putative enhancer elements. To provide insights into the regulatory role of enhancer-associated non-coding variants in cancer epigenome, and to facilitate the identification of functional non-coding mutations, we present dbInDel, a database where we have comprehensively analyzed enhancer-associated insertion and deletion variants for both human and murine samples using ChIP-Seq data. Moreover, we provide the identification and visualization of upstream TF binding motifs in InDel-containing enhancers. Downstream target genes are also predicted and analyzed in the context of cancer biology. The dbInDel database promotes the investigation of functional contributions of non-coding variants in cancer epigenome. The database, dbInDel, can be accessed from http://enhancer-indel.cam-su.org/. Supplementary data are available at Bioinformatics online.
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影响因子：
46.9
作者：
通讯作者：
--
影响因子：
64.5
作者：
Groeschel, Stefan;Sanders, Mathijs A.;Delwel, Ruud
通讯作者：
Delwel, Ruud
影响因子：
14.9
作者：
Tate JG;Bamford S;Jubb HC;Sondka Z;Beare DM;Bindal N;Boutselakis H;Cole CG;Creatore C;Dawson E;Fish P;Harsha B;Hathaway C;Jupe SC;Kok CY;Noble K;Ponting L;Ramshaw CC;Rye CE;Speedy HE;Stefancsik R;Thompson SL;Wang S;Ward S;Campbell PJ;Forbes SA
通讯作者：
Forbes SA
影响因子：
30.8
作者：
Zhang W;Bojorquez-Gomez A;Velez DO;Xu G;Sanchez KS;Shen JP;Chen K;Licon K;Melton C;Olson KM;Yu MK;Huang JK;Carter H;Farley EK;Snyder M;Fraley SI;Kreisberg JF;Ideker T
通讯作者：
Ideker T
DOI：
10.1126/science.1259037
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Mansour MR;Abraham BJ;Anders L;Berezovskaya A;Gutierrez A;Durbin AD;Etchin J;Lawton L;Sallan SE;Silverman LB;Loh ML;Hunger SP;Sanda T;Young RA;Look AT
通讯作者：
Look AT