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

Introduction

The 'Mutations on Genes' displays SNVs and InDels with their coordinates and function annotations along the selected transcript of a given gene. Mutation information can be viewed in three levels (genome, cDNA, and peptide). Different icons are applied to mutations according to their types and function changes, such as synonymous and missense SNV, frame-shift InDels. Interactive tooltip gives more information, including mutation coordinates, function area and details of exons. Sidebar offers options to adjust displays, such as changing resolution, and selecting mutation. This visualization is commonly utilized to show the mutation landscape of given genes in a group of cancer samples.

Input Files

Check the official demo input here.

Mutation File

Note that backend annotation task will be activated once the mutation file is uploaded. User could check the job status in task monitor at the bottom of this page.
This input file could be standard MAF file (see format) or VCF file.
Or, a simple CSV file in format specified below.

#SampleID alt_type chr pos ref_allele alt_allele gene
TCGA-AK-3451 SNP chr3 10183646 G A VHL
  • the first line should be the header as specified above.
  • # prefix is mandatory to indicate the header line.
  • currently, alt_type allows SNP, DEL, and INS.

Depth TSV BGZ File (Optional)

User could upload a tsv.bgz compressed file to supply the depth distribution of the gene region.
The uploaded file must match the required format as specified below.

#chr pos depth
chr1 10182642 100
  • the first line should be the header as specified above.
  • # prefix is mandatory to indicate the header line.
  • chr and pos respectively stand for the chromosome and position of the mutation.
  • depth is the sequencing depth at this genomic position.

The TSV file must be sorted by chromosome and position, and compressed by bgzip tools for tabix indexing to support fast data processing at the backend of Oviz-Bio.
For example, run the following command in the linux terminal (bgzip installed): 

(head -1 depth.tsv; sed -n '2,$p' depth.tsv | sort -k1,1 -k2n) | bgzip -c > depth.tsv.bgz

Display Interactions

  • Highlights
    • exons will be highlighted in three levels (DNA, cDNA, peptide) simultaneously.
    • mutation guide line will be highlighted to link mutated locations in the three levels.
  • Tooltips
    Tooltips will show necessary information of object that the mouse points to.
    • exon: NO., interval, transcript, sense strand, sample amount having mutation in this exon.
    • mutation: mutation details, sample(s) involved.
  • Level exchange
    • the main display level can be changed via clicking the level name.
  • Annotation
    • mutation are denoted by icons according to classification and function change type.
    • domains are displayed on protein level of available transcript.
  • Zoom in/out
    the main display level can be zoomed in/out via mouse wheel.
  • Pages
    click 'Prev' or 'Next' to go to other genes (as listed in the Mutation 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
    • Genes: select transcript for each gene.
    • Mutations: enable or disable to display certain mutations.
    • Exons: reset resolution for each exon.
  • Setting
    • select gene to display.
    • extend certain interval bilaterally from the gene body.
    • enbale or disable displaying of exon NO.
    • reset the Intron:Exon displaying resolution scale in DNA level.
    • reset the UTR:CDS displaying resolution scale in cDNA level.
    • enbale or disable displaying depth spectrum.

Manual version=1.5

  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 2a)
  2. Zhang, L., Zhou, Y., Cheng, C., Cui, H., Cheng, L., Kong, P., ... & Wang, F. (2015). Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma. The American Journal of Human Genetics, 96(4), 597-611. (PMID: 25839328, See Figure 3B)
  3. Gao, Y., Chen, Z., Li, J., Hu, X., Shi, X. J., Sun, Z., ..., Gao, S. and He, J. (2014). Genetic landscape of esophageal squamous cell carcinoma. Nature Genetics, 46(10), 1097. (PMID: 25151357, See Figure 2 and Figure 3)
  4. Li, X., Wu, W. K., Xing, R., Wong, S. H., Liu, Y., Fang, X., ... & Zhou, Y. (2016). Distinct subtypes of gastric cancer defined by molecular characterization include novel mutational signatures with prognostic capability. Cancer research, 76(7), 1724-1732. (PMID: 26857262, See Figure 3)
  5. Cancer Genome Atlas Research Network, et al. (2017). Integrated genomic and molecular characterization of cervical cancer. Nature, 543(7645), 378. (PMID: 28112728, See Extended Data Figure 2)
  6. Ojesina, A. I., Lichtenstein, L., Freeman, S. S., Pedamallu, C. S., Imaz-Rosshandler, I., Pugh, T. J., ..., Salvesen, H. B. and Meyerson, M. (2014). Landscape of genomic alterations in cervical carcinomas. Nature, 506(7488), 371. (PMID: 24390348, See Figure 2)

Version

v1.0.7 (2020-08-15)

Developer

Mr. LI Hechen (GitHub)
Miss. LI Shiying (GitHub)

Designer

Dr. JIA Wenlong (Scholar, ORCID, GitHub)

Updates

v1.0.7

  • use global exon number instead of index on protein layer.
  • resolve quotation marks in exported csv file.
  • apply the lollipop style.
  • add information text frame of mutation icons.

v1.0.6

  • add manual selection of samples.
  • add quick selection of mutation types.

v1.0.5

  • refine the mutation legend.
  • refine colour settings.
  • add colour themes of cBioPortal and scientific journals.
  • refine exon numbers of negative strand gene.
  • show exon number in default.
  • support MAF and VCF input file.

v1.0.4

  • fix page refreshing when a task finishes.
  • fix job name link in task monitor.
  • change 'Depth File' as optional input.
  • fix displaying of the transcript without domains.
  • allow hiding the depth spectrum.

v1.0.3

  • task monitor for mutation annotation.
  • display AA changes on the protein level.
  • update mutation icons.
  • fix sidebar transcript selection.
  • fix the exon interval display on each level.
  • fix the current range display of the minus-strand gene.
  • fill the exon gap on cDNA and protein levels.

v1.0.2

  • summarize samples at same mutation.
  • move tooltip to mutation icon.
  • debug with gene sense strand.

v1.0.1

  • initial functions implemented.
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