Computational protocol: Multigenic nature of the mouse pulmonary adenoma progression 1 locus

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Protocol publication

[…] Correlation was assessed using Spearman's rank correlation coefficient. Analysis of sex differences in lung tumor multiplicity was carried out using Welch’s t test. Statistical procedures were carried out using R or the “Rcmdr” library in R [] and all statistical tests were two-sided.Associations between SNPs and N2lung were assessed with PLINK software, using qfam, a family-based association test for quantitative traits. This test performs a simple linear regression of phenotype on genotype, and then uses a special permutation procedure to correct for family structure and to calculate empirical P-values []. These analyses were adjusted by sex. Linkage disequilibrium analyses between markers were also carried out using PLINK. Manhattan plots were generated using the “gap” library in R. […]

Pipeline specifications

Software tools PLINK, FBAT
Application GWAS
Organisms Mus musculus, Homo sapiens
Diseases Adenoma, Lung Neoplasms, Neoplasms
Chemicals Urethane