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

Introduction

The 'Phased on Genes' displays phased haplotypes of 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 haplotype landscape of given genes in a group of cancer samples.

Currently, we demonstrate the phasing results from two phasing tools, CNAHap and HLAPro.

Input Files by CNAHap

Check the official demo input in the sidebar (reference: hg38, Demo File Sets).

Phased Mutation File

Note that backend annotation task will be activated once the phased mutation file is uploaded. User could check the job status in task monitor at the bottom of this page.
This input file a simple CSV file in format specified below.

#SampleID alt_type chr pos ref_allele alt_allele gene phase CN M m
TCGA-AK-3451 SNP chr3 10183646 G A VHL 1\ 0 3 2
  • 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.
  • phase store the phasing information with VCF format.
  • CN, M, and m means the total, major, and minor copy number of given mutation, respectively.

Gene Sample File

Gene sample file is a simple CSV file which stores the sample gene meta information.

gene sample c_phased nmutnum nmutdensity ntotalcn nmajorcn
VHL TCGA-AK-3451 TRUE 2 0.000106 3 2
  • The first line should be the header as specified above.
  • The header of the first and second columns must be gene and sample.
  • The subsequent headers should be with prefix c_ and n_ as categorical and numerical meta information, respectively.

Input Files by HLAPro

Check the official demo input in the sidebar (reference: hla, Demo File Sets).

Phased Mutation file

Note that backend annotation task will be activated once the phased mutation file is uploaded. Us er could check the job status in task monitor at the bottom of this page.
This input file a simple CSV file in format specified below.

| #SampleID | alttype | chr | pos | refallele | alt_allele | gene | phase | CN | M

m
  • | ---- | | NA12878 | SNP | HLAA | 1235 | G | T,C | HLAA | 1|2 | 2 | 1
    | 1 |

  • 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.

  • phase store the phasing information with VCF format.

  • CN, M, and m means the total, major, and minor copy number of given mutation, respectivel y.

Gene Sample File

Gene sample file is a simple CSV file which stores the sample gene meta information.

gene sample c_phased nmutnum nmutdensity c_pedigree
HLA_A NA12878 TRUE 27 0.00771 Child
  • The first line should be the header as specified above.
  • The header of the first and second columns must be gene and sample.
  • 'c_pedigree' allows 'Father', 'Mother', 'Child', 'Unknown'.
  • The subsequent headers should be with prefix c_ and n_ as categorical and numerical meta information, respectively.

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

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