MPGK: A user-friendly tool for Mendelian randomization, polygenic risk score, Geno Ontology, and the Kyoto Encyclopedia of Genes and Genomes analysis

<h4>Background</h4>Mendelian randomization (MR), polygenic risk score (PRS), Geno Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) are powerful bioinformatic analysis tools. However, the analysis of MR, PRS, GO, and KEGG may pose a challenge for novices. This article intends to introduce a program that adeptly guides beginners in implementing these analysis functions, ensuring that even those new to the field can confidently use them.<h4>Methods</h4>The MPGK program was developed to run on the command line. It conveniently implements the MR, PRS, GO, and KEGG analysis functions by calling well-written R programs. The results of our analyses were validated using genome-wide association study (GWAS) summary data for diabetes and psoriasis, as well as gene sequencing data for diabetes.<h4>Results</h4>Three demo analyses using the MPGK program demonstrate the comprehensive capabilities of the MPGK program in conducting advanced bioinformatics analysis. First, the MPGK program revealed a causal relationship between diabetes and psoriasis. Additionally, the PRS analysis generated polygenic risk scores for diabetes, demonstrating the implementation of PRS analysis within the MPGK framework. Furthermore, the GO and KEGG analyses indicated that psoriasis is associated with infection and T helper 17 cells. These findings are consistent with the previous literature.<h4>Conclusion</h4>MPGK can be easily used to perform comprehensive analysis, including MR, PRS, GO, and KEGG analyses, by both beginners and researchers.