dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq

Moli Huang; Yunpeng Wang; Manqiu Yang; Jun Yan; Henry Yang; Wenzhuo Zhuang; Ying Xu; H Phillip Koeffler; De-Chen Lin; Xi Chen

doi:10.1093/bioinformatics/btz770

dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq

Bioinformatics. 2020 Mar 1;36(5):1649-1651. doi: 10.1093/bioinformatics/btz770.

Authors

Moli Huang^{1

2}, Yunpeng Wang¹, Manqiu Yang¹, Jun Yan³, Henry Yang⁴, Wenzhuo Zhuang¹, Ying Xu², H Phillip Koeffler^{4

5}, De-Chen Lin⁵, Xi Chen⁶

Affiliations

¹ Department of Bioinformatics, School of Biology and Basic Medical Sciences.
² Cambridge-Suda Genomic Research Center, Soochow University, Suzhou 215123, China.
³ MOE Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China.
⁴ Cancer Science Institute of Singapore, National University of Singapore, Singapore 119074, Singapore.
⁵ Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
⁶ Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.

Abstract

Summary: 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.

Availability and implementation: The database, dbInDel, can be accessed from http://enhancer-indel.cam-su.org/.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromatin Immunoprecipitation Sequencing
Enhancer Elements, Genetic*
Genome-Wide Association Study*
Genomics
Humans
Mice
Protein Binding