KGGSEE User Manual

Miaoxin Li, Lin Jiang, Xiangyi Li, and Lin Miao

KGGSEE (a biological Knowledge-based mining platform for Genomic and Genetic association Summary statistics using gEne Expression) is a standalone Java application for knowledge-based mining of GWAS summary statistics. It performs:

1. Phenotype-gene/transcript association test: GATES (Li et al. 2011) and ECS (Li et al. 2019)

2. Phenotype’s driver-cell type/driver-tissue inference: DESE (Jiang et al. 2019) and eDESE (Li et al. 2022)

3. Gene/transcript expression causal effect inference: EMIC (Jiang et al. 2022)

4. Gene/transcript heritability estimation: EHE (Miao et al. 2023)

Contents:

• Setup
  • System requirements
  • Setup a Java Runtime Environment (JRE)
  • KGGSEE and its running resources
  • Set up an environment for the Quick tutorials
  • Set up an environment for customized analyses
• Quick tutorials
  • GATES and ECS (gene-based association tests)
    • Options and input files
    • Output files
  • DESE (driver-tissue inference)
    • Options and input files
    • Output files
  • EMIC (gene-expression causal-effect inference)
    • Options and input files
    • Output files
  • EHE (gene-based heritability estimation)
    • Options and input files
    • Output files
• Detailed Document
  • GATES and ECS (gene-based association tests)
    • Synopsis
    • Examples
      • Test based on physical distance
      • Test guided by eQTLs of a gene
      • Test guided by eQTLs of a transcript
    • Outputs
  • DESE (driver-tissue inference)
    • Synopsis
    • Examples
      • DESE based on physical distance (eDESE:dist)
      • DESE guided by eQTLs (eDESE:gene and eDESE:isoform)
      • DESE for drug prioritization analysis
    • Outputs
  • EMIC (gene-expression causal-effect inference)
    • Synopsis
    • Examples
      • Gene-expression causal-effect inference
      • Transcript-expression causal-effect inference
    • Outputs
  • EHE (gene-based heritability estimation)
    • Synopsis
    • Examples
      • Gene heritability based on physical distance
      • Gene heritability guided by eQTLs
      • Transcript heritability guided by eQTLs
      • Gene’s conditional heritability based on physical distance
    • Outputs
• Options
  • Reference population genotypes
  • GWAS summary statistics
  • Global misc
  • GATES and ECS
  • DESE
  • EMIC
  • EHE
• Citations