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. Methylation information panel
    • 2.1.4. Gene expression panel (IMM 3cell analysis)
    • 2.1.5. Gene Expression Panel (ToMMo ISO-Seq)
    • 2.1.6. Genome browser panel
    • 2.1.7. GWAS analysis results panel
    • 2.1.8. HLA allerle frequency panel
    • 2.1.9. 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. Genome browser
  • 2.6. Metabolite page
    • 2.6.1. Metabolite information panel
    • 2.6.2. Concentration distribution panel
    • 2.6.3. Pregnant - non-pregnant comparison panel
    • 2.6.4. Repeat assessment panel
    • 2.6.5. Metabolite correlation panel
    • 2.6.6. GWAS panel
  • 2.7. Metabolite Correlation Network Viewer
    • 2.7.1. How to launch the Metabolite Correlation Network Viewer
    • 2.7.2. Network plot panel
    • 2.7.3. Network information panel
    • 2.7.4. Metabolite information panel
  • 2.8. PGx page
    • 2.8.1. Access to PGx data
    • 2.8.2. Detail page
  • 2.9. Metagenome page
    • 2.9.1. How to access
    • 2.9.2. Search
    • 2.9.3. Expansion to the specific level
    • 2.9.4. Expand or collapse lower-level items
    • 2.9.5. Jump to a detail page
    • 2.9.6. Detail page
  • 2.10. GWAS page
    • 2.10.1. Structure of GWAS pages
    • 2.10.2. GWAS study detail page
    • 2.10.3. GWAS analysis result detail page
    • 2.10.4. GWAS trait detail page
  • 2.11. Download page
    • 2.11.1. Downloading files
    • 2.11.2. Downloading files that require DTA acceptance
  • 2.12. Tips: how to work with DataTable
    • 2.12.1. Keyword search
    • 2.12.2. Column selector
    • 2.12.3. Save as CSV
    • 2.12.4. Sort
    • 2.12.5. Filtering
  • 2.13. Tips: Preference page
    • 2.13.1. Genome → Reference Genome Sequence
    • 2.13.2. Genome → Genome Variation Name style
    • 2.13.3. Gene → Gene model
    • 2.13.4. Miscellaneous → Loading indicator
• 3. Details of datasets included in jMorp
  • 3.1. JG2.1.0
  • 3.2. 38KJPN
  • 3.3. 38KJPN-HLA
  • 3.4. 8.3KJPN-SV
  • 3.5. JSV1
  • 3.6. ToMMo ISO-Seq
  • 3.7. IMM 3cell analysis
  • 3.8. IMM cord blood
  • 3.9. Proteome
  • 3.10. Metabolome 2022
  • 3.11. PGx
  • 3.12. Metagenome 16S-v4
  • 3.13. Metagenome 16S-v3/v4
  • 3.14. Data other than TMM analysis data

• References
• Contact

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