To examine the relationships between gene expression and gene structure for Arabidopsis and rice genes, I firstly calculated Spearman's rank sum correlation coefficients between various structural parameters and total expression level (Exp tot, the sum of expression quantity of a gene acrosss tissues where the gene is expressed).
Results were expressed as the percentage of normalised expression relative to the sum of expression across all tissues tested.
Unlike the significant global underexpression seen when tumors were compared to non-malignant cells, samples from Golden Retrievers showed a net increase in the sum of expression of genes located in CFA 3, CFA 25 and CFA 30, and a net reduction in the sum of expression of genes located in CFA 12, CFA 14, CFA 29, CFA 32, CFA 33, and CFA 34.
Predictably, since samples from Golden Retrievers included 3 females, this group also showed a net increase in the sum of expression of genes in the X chromosome.
Gene expression levels were calculated as ratios between the expression intensity of gene X in one particular tissue divided by sum of expression intensities of gene X in all tissues included in the analysis.
For cortex gene list, 1,000,000 random transcript lists with 87 transcripts were constructed and the sum of expression levels across each gene list was used to predict survival in a univariate Cox model and the p-value was recorded.
For each sample, we computed the weighted sum of expression of the genes of the TSTSS.
Based on that, we quantify the expression of all putative target genes by dividing the sum of expression values within these three categories by the sum of expression values in all categories.
Isoform fraction is calculated as the expression of a single isoform divided by the sum of expression of isoforms assigned to a gene.
To build the list of genes, we calculated the ratio of maximum expression to the sum of expression in all tissues across the Gene Atlas.
