Analyzing RNA expression patterns after filtering - labbces/sugarcane_RNAome GitHub Wiki

Analyzing the expression matrix after filtering

We dedicated efforts to assess the efficiency of the filtering process in retaining genes relevant to the co-expression study. In this analysis, we examined the expression patterns of gene pairs within the four quartiles of the resulting matrix after filtering, selecting four random gene pairs per quartile. This process was executed using this R script.

The expression patterns of the four quartiles in the expression matrix, generated from the Correr2022 dataset, are displayed below. This dataset is particularly interesting due to its inclusion of 12 contrasting genotypes in fiber accumulation, divided into two groups (6 genotypes classified as high biomass and 6 genotypes classified as low biomass).

It is noteworthy that the expression patterns of these gene pairs are sometimes opposite. Furthermore, the filtering process appears to be effective in selecting genes with high expression values, as evidenced by the increase of expression level in the fourth quartile.