Download and Check the Virus Integration CSV input.

Introduction

Nearly 20% of human cancers are related to viral infection, especially the oncovirus, which is found commonly integrate into the host genome, and cause genome instability and higher risks to develop cancers, such as human papillomavirus (HPV) in cervical carcinoma and hepatitis B virus (HBV) in liver cancer. So far, many viral integration hotspot genes are found in oncovirus studies. We implement the Virus: Integ HotSpot visualization to illustrate the oncovirus integrated hotspot of group samples in a genome browser way. Oviz-Bio automatically calculates the hotspot genomic regions from the virus integration list submitted by users.

Input Files

Virus Integration CSV File

Check the official demo input here.
The uploaded CSV file must match the required format as specified below.

  • header
    The header should follow the following format:
#SampleID Chr Position Strand JR_count
T9202 chr8 128276003 - 13

Display Interactions

  • Tooltips
    Tooltips will show necessary information of object that the mouse points to.
    • integraion: SampleID, integration position, junction strand.
    • gene: transcript name, interval.
    • exon: NO., interval.
    • annotation: details of objects displayed in the annotation panel.
  • Zoom in/out
    the main display level can be zoomed in/out via mouse wheel.
  • Pages
    click 'Prev' or 'Next' to go to other hotspot loci.
  • Download
    One SVG file will be generated when the 'Download' button is clicked. Two themes are supplied: the default theme with a dark background and the light theme with white background. To use the light theme, please click the 'Light Theme' button.

Sidebar Functions

  • Files
    • Manage Files: checklist of files uploaded previously, delete or download files.
    • Upload: upload files. Note that the duplicated file name will be alerted and given a random postfix.
    • Choose: choose files uploaded previously. Note that this function is ONLY available to registered users (each account has certain storage).
    • File Sets: save multiple files together as a file set. User can also choose to apply one file set previously saved.
  • Data
    • Hotspots: select to show integrations in current page.
    • Genes: select transcript for each gene or disable.
    • Leftouts: check integrations that cannot form hotspot region.
  • Annotation Panel
    select annotation database.
  • Setting
    • reset the interval size used in connecting integrations to form hotspot loci.
    • select hotspot locus to display.
    • select either strand to show genes.
    • merge gene track to get condensed displaying.
    • show one sample only one time in current page.
    • display gene name rather than transcript name.
    • display all genes.
    • color the integration icon with junction strand.
    • show the leftout integrations in addtional pages.

Manual version=1.1, written by Dr. JIA Wenlong on 2020-02-26.

  1. Sung, W. K., Zheng, H., Li, S., Chen, R., Liu, X., Li, Y., ... & Mulawadi, F. H. (2012). Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nature genetics, 44(7), 765. (PMID: 22634754, See Figure 3)
    Demo File: HBV_PMID22634754.csv
  2. Hu, Z., Zhu, D., Wang, W., Li, W., Jia, W., Zeng, X., ..., Wang, H. and Ma, D. (2015). Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism. Nature Genetics47(2), 158. (PMID: 25581428, See Figure 3)
    Demo File: HPV_PMID25581428.csv

Version

v1.0.3 (2020-02-24)

Developer

Mr. LI Hechen (GitHub)

Designer

Dr. JIA Wenlong (Scholar, ORCID, GitHub)

Updates

v1.0.3

  • show strand color in minimap.
  • refine display of single strand.
  • refine info at the bottom left.
  • refine display during page refresh.
  • apply compressed data transmission.
  • refine the interval calculation.
  • add gene info in tooltip of integration arrow.
  • show text frame when arrow is clicked.

v1.0.2

  • always show trans_name in tooltip.
  • default to hide the Annotation Track.
  • show page info at the bottom left.

v1.0.1

  • initial functions implemented.
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