KGG:A systematic biological Knowledge-based mining system for Genome-wide Genetic studies
KGG 2.5 Demo Video
 MX Li's tools:
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 5 types of secondary analyses:
  Gene-based association;
  Conditional gene-based association;
  Multivariate gene-based association;
  Gene-pair-based association;
  Gene-set-based association.
In addtion, it also provides hyperlinks to several useful bioinformatics annotation databases on sequence variants (GWASrap), genes (GeneCards) and pathways (MsigDB).

New analysis procedure in the KGG4.0. Please read the user-manual of KGG4 for details.

References & Citations:
    1. 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. PubMed      AJHG
    2. 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. PubMed      AJHG
    3. 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. PubMed      Plos One
    4. 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. PubMed      Bioinformatics
    5. Li et al. A powerful approach isolates independently associated genes of Schizophrenia with summary statistics from large-scale whole genome association meta-analysis (Submitted)
    6. Gui et al. Genome-wide gene- and gene-set-based association analyses identify novel patterns of genetic sharing across complex phenotypes(Submitted)

Miao-xin Li, Zhongshan School of Medicine,Sun Yat-sen University && Centre for Genomic Sciences, The University of Hong Kong, All rights reserved.