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Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing.

Yang X, Li M, Liu Q, Zhang Y, Qian J, Wan X, Wang A, Zhang H, Zhu C, Lu X, Mao Y, Sang X, Zhao H, Zhao Y, Zhang X - Nucleic Acids Res. (2014)

Bottom Line: A total of 2295 integration sites are located near 1730 involved genes.Of the VISes, 1153 are detected in the exons or introns of genes, with 294 located up to 5 kb and a further 112 located up to 10 kb away.As viral integration may alter chromosome stability and gene expression levels, characterizing VISes will contribute toward the discovery of novel oncogenes, tumor suppressor genes and tumor-associated pathways.

View Article: PubMed Central - PubMed

Affiliation: Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China.

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Related in: MedlinePlus

The flow scheme for setting up the Dr.VIS v2.0 and the overview of the database. Abbreviations: HBV, hepatitis B virus; EBV, Epstein–Barr virus; HHV, human herpesvirus ; HPV, human herpesvirus; MCV, Merkel cell polyomavirus; HIV, human immunodeficiency virus; HTLV, human T lymphotropic virus; XMRV, xenotropic murine leukemia virus-related virus.
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Figure 1: The flow scheme for setting up the Dr.VIS v2.0 and the overview of the database. Abbreviations: HBV, hepatitis B virus; EBV, Epstein–Barr virus; HHV, human herpesvirus ; HPV, human herpesvirus; MCV, Merkel cell polyomavirus; HIV, human immunodeficiency virus; HTLV, human T lymphotropic virus; XMRV, xenotropic murine leukemia virus-related virus.

Mentions: Data collection and annotation for Dr.VIS v2.0 was carried out in a similar fashion as for version 1.0 (18). In recent times, the growth of papers reporting VISes has been rapid. To keep up with this, we systematically collected newly described VISes and curated related information (Figure 1). We first carried out a PubMed literature search using a list of keywords pertaining to virus integration, including ‘virus integration’, ‘virus integration site’, ‘virus integration sequence’, ‘virus integration tumor’ and ‘cancer and disease’. We then extracted more VISes keywords from this literature and filtered the downloaded files using these keywords. The filtered entries were subsequently confirmed by manual curation (Figure 1).


Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing.

Yang X, Li M, Liu Q, Zhang Y, Qian J, Wan X, Wang A, Zhang H, Zhu C, Lu X, Mao Y, Sang X, Zhao H, Zhao Y, Zhang X - Nucleic Acids Res. (2014)

The flow scheme for setting up the Dr.VIS v2.0 and the overview of the database. Abbreviations: HBV, hepatitis B virus; EBV, Epstein–Barr virus; HHV, human herpesvirus ; HPV, human herpesvirus; MCV, Merkel cell polyomavirus; HIV, human immunodeficiency virus; HTLV, human T lymphotropic virus; XMRV, xenotropic murine leukemia virus-related virus.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383912&req=5

Figure 1: The flow scheme for setting up the Dr.VIS v2.0 and the overview of the database. Abbreviations: HBV, hepatitis B virus; EBV, Epstein–Barr virus; HHV, human herpesvirus ; HPV, human herpesvirus; MCV, Merkel cell polyomavirus; HIV, human immunodeficiency virus; HTLV, human T lymphotropic virus; XMRV, xenotropic murine leukemia virus-related virus.
Mentions: Data collection and annotation for Dr.VIS v2.0 was carried out in a similar fashion as for version 1.0 (18). In recent times, the growth of papers reporting VISes has been rapid. To keep up with this, we systematically collected newly described VISes and curated related information (Figure 1). We first carried out a PubMed literature search using a list of keywords pertaining to virus integration, including ‘virus integration’, ‘virus integration site’, ‘virus integration sequence’, ‘virus integration tumor’ and ‘cancer and disease’. We then extracted more VISes keywords from this literature and filtered the downloaded files using these keywords. The filtered entries were subsequently confirmed by manual curation (Figure 1).

Bottom Line: A total of 2295 integration sites are located near 1730 involved genes.Of the VISes, 1153 are detected in the exons or introns of genes, with 294 located up to 5 kb and a further 112 located up to 10 kb away.As viral integration may alter chromosome stability and gene expression levels, characterizing VISes will contribute toward the discovery of novel oncogenes, tumor suppressor genes and tumor-associated pathways.

View Article: PubMed Central - PubMed

Affiliation: Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China.

Show MeSH
Related in: MedlinePlus