Miaoxin Li; Lin Jiang; Chao Xue; Jaing Li
KGG (Knowledge-based mining system for Genome-wide Genetic studies) is a software tool to perform knowledge-based secondary analyses of p-values from genome-wide association studies (GWAS). The knowledge-based secondary analyses include gene-based, gene-pair-based and gene-set based association analysis.It is implemented by Java with a user-friendly graphic interface to facilitate data analysis and result visualization. Build on advanced algorithms, it is able to process up to 10 million variants in several hours with 15GB RAM on a workstation. KGG4 currently provides 6 types of secondary analyses:
- Gene-based association
- Conditional gene-based association
- Multivariate gene-based association
- Gene-pair-based association
- Gene-set-based association
- Driver-tissue estimation
For details and an executable version of KGG, see http://grass.cgs.hku.hk/limx/kgg.
- Li MX, Kwan JS, Sham PC. HYST: A HYbrid Set-based Test for genome-wide association studies, with application to protein-protein interaction-based association analysis. Am J Hum Genet. 2012 Sep 7;91(3):478-88.
- Li MX, Gui HS, Kwan JS, Sham PC. GATES: A rapid and powerful gene-based association test using extended Simes procedure. Am J Hum Genet. 2011 Mar 11;88(3):283-293.
- Li MX, Sham PC, Cherny SS, Song YQ.(2010) A knowledge-based weighting framework to boost the power of genome-wide association studies. PLoS One Dec 31;5(12):e14480.
- Van der Sluis S, Dolan CV, Li J, Song Y, Sham P, Posthuma D, Li MX. MGAS: a powerful tool for multivariate gene-based genome-wide association analysis. Bioinformatics 2015 Apr 1;31(7):1007-15.
- Li et al. A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia. Bioinformatics 2019 Feb 15;35(4):628-635.
- Gui et al. Sharing of Genes and Pathways Across Complex Phenotypes: A Multilevel Genome-Wide Analysis. Genetics 2017 Jul;206(3):1601-1609
- Jiang et al. Estimating driver-tissues by selective expression of genes associated with complex diseases or traits (submitted)
The code is released under MIT License.