What are DEGs?

DEG stands for differentially expressed gene. The difference of gene expression is statistically significant between treatment and control groups for each DEG.

Treatment and control groups

We used three groups - L1, L2 and L3 diets - to calculate DEGs. L1 diet was used as control.

Data sets for differential expression analysis

• L2:L1: L2 vs. L1 with using L1 as control
• L3:L1: L3 vs. L1 with using L1 as control

See Experimental feed for details about L1, L2 and L3 groups.

Statistical calculation

We used DESeq2 to calculate LFCs (log-fold changes) and adjusted p-values. Positive LFCs indicate up-regulation, whereas negative LFCs indicate down-regulation based on the L1 expression level. We used the following criteria to define our DEGs.

1. abs(LFC) >= 0
2. Adjusted p-value < 0.1

Differentially expressed genes

L3 diet affected gene expression profiles more than L2 diet in terms of the number of DEGs.

Identified DEGs for L2:L1 and L3:L1

• L2 vs. L1: 6 DEGs
• L3 vs. L1: 97 DEGs

Volcano plots of differentially expressed genes in L2:L1 and L3:L1.

List of DEGs

• List of DEGs - L2 vs. L1
• List of DEGs - L3 vs. L1
• Excel files (Downloads page)