jMorp User Guide

Attention

This document is a work-in-progress document explaining how to use the jMorp website, and some pages may not be fully described. We are updating it as needed.

Attention

The English version of the jMorp User Guide was generated based on a machine translation of the Japanese version . There could be some incorrect sentences.

Table of contents

• 1. Overview of jMorp
  • 1.1. What is jMorp?
  • 1.2. Datasets included in jMorp
  • 1.3. Website structure
  • 1.4. Access to datasets in the database
    • 1.4.1. Keyword search
    • 1.4.2. Genome browser view
    • 1.4.3. Category index
  • 1.5. The layout of item pages
• 2. How to use jMorp website
  • 2.1. Gene page
    • 2.1.1. Gene information panel
    • 2.1.2. SNV/INDEL panel
    • 2.1.3. SNV/INDEL density panel
    • 2.1.4. CNV panel
    • 2.1.5. STR Panel
    • 2.1.6. Methylation information panel
    • 2.1.7. Gene expression panel (ToMMo whole blood)
    • 2.1.8. Gene expression panel (IMM 3cell analysis)
    • 2.1.9. Gene expression panel (ToMMo ISO-Seq)
    • 2.1.10. Genome browser panel
    • 2.1.11. GWAS analysis results panel
    • 2.1.12. HLA allerle frequency panel
    • 2.1.13. PGx panel
  • 2.2. SNV/INDEL page
    • 2.2.1. Basic information panel
    • 2.2.2. Allele / genotype frequency panel
    • 2.2.3. Gene annotation panel
    • 2.2.4. dbNSFP score panel
    • 2.2.5. GWAS analysis results panel
    • 2.2.6. LiftOver panel
  • 2.3. SNV/INDEL allele frequency comparison tool
  • 2.4. SNV/INDEL protein structure mapping tool
    • 2.4.1. Basic usage
    • 2.4.2. Switch to the mapping results page for protein structures in AlphaFold DB
  • 2.5. CNV page
    • 2.5.1. Directions to CNV page
    • 2.5.2. CNV page content
  • 2.6. STR Page
    • 2.6.1. Directions to STR page
    • 2.6.2. STR page content
  • 2.7. Genome Browser
    • 2.7.1. Open Genome Browser
    • 2.7.2. The list of tracks
    • 2.7.3. Region search
    • 2.7.4. Overlay your data.
    • 2.7.5. How to display variant co-occurrence
    • 2.7.6. Share the contents of the display with others
    • 2.7.7. Compare two reference genomes
    • 2.7.8. JBrowse official document
  • 2.8. Metabolite page
    • 2.8.1. Metabolite information panel
    • 2.8.2. Concentration distribution panel
    • 2.8.3. Postprandial changes panel
    • 2.8.4. Pregnant - non-pregnant comparison panel
    • 2.8.5. Repeat assessment panel
    • 2.8.6. Metabolite correlation panel
    • 2.8.7. GWAS panel
    • 2.8.8. Metabolic index panel
  • 2.9. Metabolite Correlation Network Viewer
    • 2.9.1. How to launch the Metabolite Correlation Network Viewer
    • 2.9.2. Network plot panel
    • 2.9.3. Network information panel
    • 2.9.4. Metabolite information panel
  • 2.10. MRI page
    • 2.10.1. Field information panel
    • 2.10.2. Volume distribution panel
    • 2.10.3. Repeat assessment panel
    • 2.10.4. Volume distribution summary panel
  • 2.11. PGx page
    • 2.11.1. Access to PGx data
    • 2.11.2. Detail page
  • 2.12. Metagenome page
    • 2.12.1. How to access
    • 2.12.2. Search
    • 2.12.3. Expansion to the specific level
    • 2.12.4. Expand or collapse lower-level items
    • 2.12.5. Jump to a detail page
    • 2.12.6. Detail page
  • 2.13. GWAS page
    • 2.13.1. Structure of GWAS pages
    • 2.13.2. GWAS study detail page
    • 2.13.3. GWAS analysis result detail page
    • 2.13.4. GWAS trait detail page
  • 2.14. Download page
    • 2.14.1. Downloading files
    • 2.14.2. Downloading files that require DTA acceptance
  • 2.15. Tips: how to work with DataTable
    • 2.15.1. Keyword search
    • 2.15.2. Column selector
    • 2.15.3. Save as CSV
    • 2.15.4. Sort
    • 2.15.5. Filtering
  • 2.16. Tips: Preference page
    • 2.16.1. Genome → Reference Genome Sequence
    • 2.16.2. Genome → Genome Variation Name style
    • 2.16.3. Gene → Gene model
    • 2.16.4. Miscellaneous → Loading indicator
• 3. Details of datasets included in jMorp
  • 3.1. JG2.1.0
  • 3.2. JG3.0.0
  • 3.3. 38KJPN-SNV/INDEL
  • 3.4. 8.3KJPN mtDNA variants panel
  • 3.5. 38KJPN-HLA
  • 3.6. 54KJPN-SNV/INDEL
  • 3.7. 54KJPN-HLA (v20230626)
  • 3.8. 54KJPN-HLA (v20230828)
  • 3.9. 54KJPN-STR
  • 3.10. JCNVv1
  • 3.11. 8.3KJPN-SV
  • 3.12. JSV1
  • 3.13. ToMMo whole blood transcriptome (v20230828)
  • 3.14. ToMMo ISO-Seq
  • 3.15. IMM 3cell analysis
  • 3.16. IMM cord blood
  • 3.17. Proteome
  • 3.18. Metabolome 2022
  • 3.19. Metabolome 2023
  • 3.20. MRI (v20240325)
  • 3.21. PGx
  • 3.22. Metagenome 16S-v4
  • 3.23. Metagenome 16S-v3/v4
  • 3.24. Metagenome shotgun
  • 3.25. Data other than TMM analysis data

• References
• Contact

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