1.3. Website structure

The jMorp website is organized as follows:

../../_images/website_structure.en.png
  • Top page
    • Batch search of entries in jMorp

    • Index for categories

  • Gene page
    • Gene ID & name

    • SNV/INDEL list & allele frequency information

    • Methylation Information

    • Gene expression information

    • Genome browser

    • GWAS analysis Information

  • SNV/INDEL page
    • dbSNP and ClinVar annotations

    • Tiled on Japonica Arrays

    • Allele & genotype frequency

    • Gene annotation

    • GWAS analysis Information

    • LiftOver

  • CNV page (not shown in the figure)
    • Frequency information of Copy Numbers

  • STR page (not shown in the figure)
    • Minimum, mean, median, and maximum number of repeats

  • SNV/INDEL structure mapping tool
    • Results of mapping SNV/INDEL to protein structure

  • Genome browser
    • Genome sequence (JG2.1.0)

    • SNV/INDEL

    • SV

    • Methylation

    • Genome Accessibility

  • Metabolite page
    • Compound names and links to external databases

    • Structure

    • [NMR] Automatic quantitation precision

    • [MS] m/z & retention time of metabolites and adduct ions

    • Intensity distribution (general population, repeat assessment, differences between pregnant and non-pregnant)

    • Correlation between compounds

    • GWAS analysis results

  • Metabolite correlation network viewer
    • Visualize and explore correlations between compounds as a network (graph)

  • GWAS page
    • Study summaries of GWAS analyses performed in TMM project

    • Download summary statistics files

    • Displays manhattan plot and QQ plot

  • MRI page (not shown in the figure)
    • Volume information of each brain region based on MRI brain imaging

  • PGx page
    • Genome variations on drug metabolism-related genes and metabolic activity analysis information

  • Metagenome page
    • Relative abundance of microbes is displayed by various categories (sample type, severity of periodontal disease, etc.)

  • Download page (not shown in the figure)
    • Bulk download of jMorp datasets

  • Whole genome sample repository (not shown in the figure)
    • A page presenting the short-read WGS analysis’s quality data (bases/average depth of each sample in the 50KJPN repository), as well as the accessibility of SNP arrays and metabolome data

  • Code repository (not shown in the figure)
    • Repository of software developed in TMM

To learn how to use each page, please refer to How to use jMorp website.