Last Updated: 2015/07/21　　　

Softwares and data source by Yukinori Okada, M.D., Ph.D. [HomePage]

Softwares and data source used in Okada et al. Nature (2014)

Okada Y, Wu D, Trynka G et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature doi:10.1038/nature12873 [PubMed]




Summary statistics of RA GWAS meta-analysis

• Trans-ethnic RA GWAS meta-analysis (19,234 RA cases and 61,565 conrols) [Link]
• Eurpean RA GWAS meta-analysis (14,361 RA cases and 43,923 conrols) [Link]
• Asian RA GWAS meta-analysis (4,873 RA cases and 17,642 conrols) [Link]
• Summary results of RA risk SNPs in 101 risk loci [Link]

Softwares for 1KG imputation and GWAS meta-analysis

• Perl source codes for 1KG imputation reference panel preparation [Link]
• Perl source codes for splitting GWAS data / 1KG reference panel into chuncks [Link]
• Perl source codes for handling association analysis results [Link]
• Java package for genomic control (GC) correction [Link]
• Java package for GWAS meta-analysis [Link]
• R source codes for plotting Manhattan / QQ plots of GWAS P-values [Link]

Pleiotropy analysis using GWAS catalogue database

• Curated phenotype/SNP data from the GWAS catalogue (for data downloaded on January 31, 2013) [Link]

H3K4me3 histone mark enrichment analysis for GWAS signals

• Software for enrichment analysis and histone mark data (from Raychaudhuri lab and the Broad Instiute) [Link]

Softwares and data source for in-silico pipeline to prioritize biological genes from GWAS risk loci

• Java package for calculating LD between SNPs and 1KG reference data [Link]
• R source codes for assigning LD regions to SNPs [Link]
• Perl source codes for assiging UCSC genes into LD regions [Link]


• Functional annotation of SNPs (Annovar software) [Link]
• eQTL data for PBMC (from http://genenetwork.nl) [Link]
• Cell-specific eQTL data (from ImmVar project) [Link]
• PubMed text-mining (GRAIL software) [Link]
• Protein-protein interaction analysis (DAPPLE software) [Link]
• Primary immunodificiency (PID) gene list (from Journal web site) [Link]
• Cancer somatic mutation gene list (from Journal web site) [Link]
• Knockout mouse phenotype and gene list (from Journal web site) [Link]
• Molecular pathway analysis (MAGENTA software) [Link]

Softwares and data source for GWAS-drug target overlap analysis

• Drug target gene list (from Journal web site) [Link]
• Perl source codes for overlap enrichment analysis [Link]

Okada Y, Yamamoto K, Yamada R. Estimation of the Null Distribution of Fisher’s Exact Test P-values in GWA Studies. ASHG Meeting (2009)




Estimation of null distribution of Fisher's exact test P-values for 2x2 SNP tables in GWAS [Poster]

• Java package for null distribution estimation [Link]