Download and Check the offical demo input.

Introduction

Fusion gene is a chimeric transcript consists of gene bodies from two or more previously separate genes. Many fusion genes have been found to contribute tumorigenesis of multiple cancer types. We implement the Fusion Genes visualization to show the whole structure of chimeric transcript structure.

Input Files

Fusion TSV File

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

  • header
    The header should follow the following format:
#Sample-ID up_gene up_chr up_pos up_covlen down_gene down_chr down_pos down_covlen
T003 FGFR3 chr4 1808661 886 TACC3 chr4 1739325 704
  • up_covlen and down_covlen respectively stand for the distance fusion supporting reads extend from the junction position of upstream (5') and downstream (3') fusion partern genes.
  • up_pos and down_pos are coordinates in the genome.
  • see more relevant information from SOAPfuse wiki page.

Display Interactions

Reference normal gene body of fusion partners are displayed with junction positions marked.

  • Tooltips
    • exon: NO., interval, and length.
  • Pages
    click 'Prev' or 'Next' to go to other genes (as listed in the Fusion TSV File).
  • 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 To check exons information of fusion genes.
  • Setting
    • enbale or disable Simplified mode.
    • display transcript name rather than gene name.

Manual version=1.0, written by Dr. JIA Wenlong on 2019-12-19.

  1. Guo, G., Sun, X., Chen, C., Wu, S., Huang, P., Li, Z., ..., Gui, Y., Wang, J. and Cai, Z. (2013). Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nature Genetics, 45(12), pp.1459-1463. (PMID: 24121792, See Figure 3a)
  2. Cancer Genome Atlas Research Network, et al. (2012). Comprehensive genomic characterization of squamous cell lung cancers. Nature489(7417), 519. (PMID: 22960745, See Figure 4)
  3. Cancer Genome Atlas Research Network, et al. (2017). Integrated genomic and molecular characterization of cervical cancer. Nature543(7645), 378. (PMID: 28112728, See Extended Data Figure 4c-d)
  4. Jia, W., Qiu, K., He, M., Song, P., Zhou, Q., Zhou, F., ... & Liao, X. (2013). SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome biology, 14(2), R12. (PMID: 23409703, See Figure 4b-e)

Version

v1.0.3 (2020-02-21)

Developer

Mr. LI Hechen (GitHub)

Designer

Dr. JIA Wenlong (Scholar, ORCID, GitHub)

Updates

v1.0.3

  • refine exon number in junction segment.
  • allow to reset bilateral length of junction segment.
  • show fusion details at bottom left.
  • allow to select transcript.
  • show domain regions on junction segment.

v1.0.2

  • show exon interal in tooltips.
  • fix display in light theme.

v1.0.1

  • initial functions implemented.
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