PLOTS PANEL
- Correlation plot: Shows the correlation between each cis-SNP and the selected gene.
- Expression plot: shows the expression profile of the selected gene by the selected covariate.
- Genotype vs expression plot: shows the expression of the selected gene vs the genotype of a selected SNP with a regression line by the selected covariate.
- Frequency table: shows the total number of samples and the number of samples for each level of the covariate.
- Correlation table: shows the correlation between the expression of the selected gene and the genotype of a selected SNP.
TABLE PANEL
A table for each cis-SNP of the selected gene is displayed and can be downloaded. The columns of the table are: the SNP, the coefficient of correlation (r2), the p.value of the association, the position of the SNP, the minor allele frequency (MAF) and the two alleles (A and B).
USAGE AND PARAMETERS
- Enter a gene name.
- Filter the values of the different available covariates.
- Choose the correlation method (Pearson or Spearman).
- Choose the range (from -2000 to 2000 Kb) to consider a SNP at a cis distance of the selected gene.
- Select the adjustment covariates.
- Select the significance threshold (0.01, 0.001, 0.0001 or Bonferroni).
- Select a SNP of interest.
- Select a MAF threshold.
- Choose a threshold for the correlation.
- Select a covariate to perform the analysis (default = tissue).
- Select an expression range: y-coordinate adjustment