Contents
What does it mean when a gene is differentially expressed?
A gene is declared differentially expressed if an observed difference or change in read counts or expression levels between two experimental conditions is statistically significant.
What is a proper threshold for deciding which genes are differentially expressed?
Somewhere between 1.1 to 1.5 is a common choice for a “sensible” threshold. But all this is getting away from the main point, which is the detection of DE genes. If you want to do this in a statistically rigorous manner, use the BH-adjusted p-values to control the false discovery rate.
How do you choose differentially expressed genes?
To select differentially expressed genes, often an investigator uses the P-value criterion to decide a cutoff threshold, which depends on the sample size and the study purpose, and then focuses on the genes that pass the cutoff with a higher fold-change for further studies.
How can differentially expressed genes be measured?
In RNA-seq studies, gene expression levels are measured by counts, i.e. by the number of reads mapped on each gene. Counts often depend on gene- and sample-specific covariates, such as gene length and library size, respectively.
What does negative logFC mean?
negative logFC indicate the logarithmic foldness of DOWNregulation. logFC = log(expr1)-log(expr2) e.g. log2FC = log2(expression in mutant backround) – log2(expression in wildtype) if a gene has an expr level of 16 in wildtype and an expr level of 4 in the mutant.
What is Z score gene expression?
Z-score: calculated by subtracting the overall average gene abundance from the raw expression for each gene, and dividing that result by the standard deviation (SD) of all of the measured counts across all samples.
How do you silence gene expression?
The genes can be silenced by siRNA molecules that cause the endonucleatic cleavage of the target mRNA molecules or by miRNA molecules that suppress translation of the mRNA molecule. With the cleavage or translational repression of the mRNA molecules, the genes that form them are rendered essentially inactive.