Please try the demo files in the sidebar (Demo File Sets).

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.

#SampleID	Chr	Position	Strand	JR_count
T9202	chr8	128276003	-	13

• the first line should be the header as specified above.
• this file is easy to prepare from the result of common virus integration detection tools.
• the Strand represents the relation DNA strand of virus integration. If the virus segment connect with host segment with different strands, the Strand value should be -, such as virus is plus strand and host is minus strand. If they connect in same strands, the Strand value should be +.
• the JR_count is the count of split-reads that support this virus integration. We consider JR_count as the credibility of this virus integration. It will be used when page trys to display only one intergration for each sample, i.e., the sidebar option Unify samples is enabled. The integration with the largest JR_count will be selected.
• note that the Gene and Comments columns in demo files are just notes, and this page will not load data of these two columns.

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=1.4, written by Dr. JIA Wenlong on 2020-04-02.