What does an MA plot tell you?

An MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.

What is Ma plot in gene expression?

MA plots are commonly used to represent log fold-change versus mean expression between two treatments (Figure 4). This is visually displayed as a scatter plot with base-2 log fold-change along the y-axis and normalized mean expression along the x-axis.

What is differential expression RNA-seq?

The next step in the RNA-seq workflow is the differential expression analysis. The goal of differential expression testing is to determine which genes are expressed at different levels between conditions. These genes can offer biological insight into the processes affected by the condition(s) of interest.

What is differential gene expression analysis?

Differential expression analysis means taking the normalised read count data and performing statistical analysis to discover quantitative changes in expression levels between experimental groups.

How do you do a MA plot?

Make MA-plot which is a scatter plot of log2 fold changes (M, on the y-axis) versus the average expression signal (A, on the x-axis). M = log2(x/y) and A = (log2(x) + log2(y))/2 = log2(xy)*1/2 , where x and y are respectively the mean of the two groups being compared.

What is FPKM value?

FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads. In RNA-Seq, the relative expression of a transcript is proportional to the number of cDNA fragments that originate from it.

What is the difference between RNA-Seq and microarray?

The main difference between RNA-Seq and microarrays is that the former allows for full sequencing of the whole transcriptome while the latter only profiles predefined transcripts/genes through hybridization.

What is HT seq?

HTSeq is a Python package that calculates the number of mapped reads to each gene.

Why is differential gene expression?

The unused genes in differentiated cells are not destroyed or mutated, and they retain the potential for being expressed. 3. Only a small percentage of the genome is expressed in each cell, and a portion of the RNA synthesized in the cell is specific for that cell type.

What is an example of gene expression?

Some simple examples of where gene expression is important are: Control of insulin expression so it gives a signal for blood glucose regulation. X chromosome inactivation in female mammals to prevent an “overdose” of the genes it contains. Cyclin expression levels control progression through the eukaryotic cell cycle.

What do volcano plots show?

A volcano plot is a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change). It enables quick visual identification of genes with large fold changes that are also statistically significant. These may be the most biologically significant genes.

What TPM is high expression?

Light blue box: expression level is low (between 0.5 to 10 FPKM or 0.5 to 10 TPM) Medium blue box: expression level is medium (between 11 to 1000 FPKM or 11 to 1000 TPM) Dark blue box: expression level is high (more than 1000 FPKM or more than 1000 TPM)