dbCID: a manually curated resource for exploring the driver indels in human cancer

Briefings in Bioinformatics
Zhenyu YueJunfeng Xia

Abstract

While recent advances in next-generation sequencing technologies have enabled the creation of a multitude of databases in cancer genomic research, there is no comprehensive database focusing on the annotation of driver indels (insertions and deletions) yet. Therefore, we have developed the database of Cancer driver InDels (dbCID), which is a collection of known coding indels that likely to be engaged in cancer development, progression or therapy. dbCID contains experimentally supported and putative driver indels derived from manual curation of literature and is freely available online at http://bioinfo.ahu.edu.cn: 8080/dbCID. Using the data deposited in dbCID, we summarized features of driver indels in four levels (gene, DNA, transcript and protein) through comparing with putative neutral indels. We found that most of the genes containing driver indels in dbCID are known cancer genes playing a role in tumorigenesis. Contrary to the expectation, the sequences affected by driver frameshift indels are not larger than those by neutral ones. In addition, the frameshift and inframe driver indels prefer to disrupt high-conservative regions both in DNA sequences and protein domains. Finally, we developed a computational method for disc...Continue Reading

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Citations

Jun 28, 2020·Briefings in Bioinformatics·Zhenyu YueJunfeng Xia
Oct 18, 2020·Interdisciplinary Sciences, Computational Life Sciences·Lingsong YaoYannan Bin

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