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Table 2 IPA downstream effects analysis performed on genes differentially expressed in distal gut of Atlantic salmon

From: Differential responses of the gut transcriptome to plant protein diets in farmed Atlantic salmon

Diet/Function Predicted activation state Activation z-score P-value Number of genesa
consistentb inconsistentc unknownd
S45 (diet with 45 % of soy protein concentrate)
 synthesis of steroid Increased 2.0 2.2E-03 4 0 4
 concentration of triacylglycerol Decreased −2.4 1.1E-03 8 1 0
B45 (diet with 45 % of bean protein concentrate)
 cell-cell adhesion Decreased −2.6 8.0E-07 7 0 7
 growth of epithelial tissue Decreased −2.4 3.2E-05 17 7 2
 development of blood vessel Decreased −2.1 3.5E-05 16 6 4
 cell movement of epithelial cells Decreased −2.0 2.7E-05 8 2 0
 cell death of smooth muscle cells Decreased −2.1 1.3E-03 6 1 0
 apoptosis of connective tissue cells Decreased −2.1 3.3E-03 8 2 1
Soybean meal (SBM) diet
 proliferation of cells Increased 2.4 4.7E-15 125 90 52
 binding of DNA Increased 2.3 1.5E-05 28 14 6
 synthesis of protein Increased 2.1 6.6E-07 22 10 12
 synthesis of lipid Increased 2.4 1.6E-06 30 15 20
 metabolism of carbohydrate Increased 2.6 1.5E-04 16 4 30
 organization of cytoplasm Increased 2.3 2.4E-04 38 21 38
 cellular homeostasis Increased 2.4 2.0E-05 43 27 37
 cell movement Increased 3.4 1.1E-07 87 47 15
 cell death Decreased −2.1 6.5E-14 124 88 36
 autophagy Increased 2.5 1.6E-04 18 6 6
  1. aGenes are listed in Additional file 10; bGenes with the direction of expression consistent with the predicted activation state of the function (e.g., gene encoding CD28 molecule is known to decrease cell proliferation and is down-regulated in the SBM dataset, therefore predicted to increase the function); cGenes with the direction of expression inconsistent with the predicted activation state of the function (e.g., gene encoding DIABLO is known to decrease cell proliferation and is up-regulated in the SBM dataset, therefore predicted to decrease the function); dGenes involved in the function with currently unknown effects