MPGK: A user-friendly tool for Mendelian randomization, polygenic risk score, Geno Ontology, and the Kyoto...

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Mendelian randomization (MR), polygenic risk score (PRS), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) are essential bioinformatics tools.
• Novice users often face challenges in performing MR, PRS, GO, and KEGG analyses.
• This study introduces a program designed to assist beginners in these advanced bioinformatics analyses.

Purpose of the Study:

• To introduce the MPGK program, a user-friendly tool for bioinformatics analysis.
• To enable beginners to confidently perform Mendelian randomization, polygenic risk score, GO, and KEGG analyses.
• To demonstrate the utility of MPGK in complex genetic and pathway analysis.

Main Methods:

• The MPGK program was developed as a command-line tool.
• It integrates MR, PRS, GO, and KEGG analyses by utilizing R programs.
• Validation was performed using genome-wide association study (GWAS) data for diabetes and psoriasis, and gene sequencing data for diabetes.

Main Results:

• MPGK successfully performed advanced bioinformatics analyses, including MR, PRS, GO, and KEGG.
• A causal link between diabetes and psoriasis was identified using MR.
• PRS analysis for diabetes was demonstrated, and GO/KEGG analyses linked psoriasis to infection and T helper 17 cells, consistent with existing literature.

Conclusions:

• The MPGK program facilitates comprehensive bioinformatics analysis for both novice and experienced researchers.
• It simplifies the execution of MR, PRS, GO, and KEGG analyses.
• MPGK empowers users to conduct advanced genetic and pathway investigations with ease.