Computational protocol: Association of VSNL1 with schizophrenia, frontal cortical function, and biological significance for its gene product as a modulator of cAMP levels and neuronal morphology

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Protocol publication

[…] Significance of the neurite outgrowth results was analyzed using Microsoft excel and Insat software. Average neurite length was expressed as mean±s.e. One-way analysis of variance was used to evaluate significant differences between treatment conditions. Sociodemographic parameters such as χ2-, t-tests or analysis of variance were used as appropriate. For case–control studies, an additive model in PLINK was used. For analyses of WCST, the covariates ‘age', ‘gender' and ‘education', as well as the ‘disease status' in the whole sample were included. Again, an additive model was calculated. Haploview 4.0 (http://www.broad.mit.edu/mpg/haploview/) was used to generate a linkage disequilibrium map (r2 and D', see ). Tests for associations using multimarker haplotypes were performed using the software environment ‘R' (http://www.R-project.org). Global and single haplotype significance and odds ratios were calculated. Nominally significant asymptotic P-values were confirmed by permuting the case–control status over 10 000 replicates to adjust for multiple testing and observing the maximum test statistic in each case. To compare quantitative traits between the haplotypes, the R software package ‘haplo.score' was used, integrating the covariates sex, age, education and diagnosis as appropriate. All nominally significant P-values were confirmed by permuting over 10 000 replicates and observing the maximum test statistic (simulated P-value; sim.p). […]

Pipeline specifications

Software tools PLINK, Haploview
Application GWAS
Organisms Rattus norvegicus, Homo sapiens