Table 2.
Comparison of fold-changes in gene expression based on RNA-seq, microarray and real time qRT-PCR results
| Gene symbol | Gene name | Gene description | RNA-seq fold-change | Array fold-change | Real time qRT-PCR fold-change |
|---|---|---|---|---|---|
|
CCL4 |
Chemokine (C-C motif) ligand 4 |
A proinflammatory and chemotactic chemokine |
40.02 |
10.53 |
26.51 |
|
CCL5 |
Chemokine (C-C motif) ligand 5 |
A proinflammatory chemokine involved in the chemotaxis of monocytes and T-helper cells |
17.43 |
14.68 |
19.12 |
|
CCL20 |
Chemokine (C-C motif) ligand 20 |
A chemokine involved in the chemoattraction of lymphocytes and neutrophils |
67.34 |
82.33 |
45.94 |
|
CD40 |
CD40 molecule, TNF receptor superfamily member 5 |
A member of the TNF-receptor superfamily. Mediates the immune and inflammatory responses |
13.43 |
9.99 |
12.32 |
|
CFB |
Complement factor B |
A component of the alternative pathway of complement activation |
3.87 |
40.63 |
40.36 |
|
CXCL2 |
Chemokine (C-X-C motif) ligand 2 |
An immunoregulatory chemokine produced by activated monocytes and neutrophils at sites of inflammation |
15.72 |
4.44 |
14.12 |
|
IL15 |
Interleukin 15 |
A cytokine that regulates T and natural killer cell activation and proliferation |
3.07 |
Not DE |
2.23 |
|
IL1B |
Interleukin 1, beta |
A cytokine that mediates the inflammatory response including cell proliferation, differentiation and apoptosis |
34.84 |
92.28 |
41.21 |
|
IL6 |
Interleukin 6 |
A cytokine that functions in inflammation and the maturation of B cells |
39.62 |
88.47 |
55.08 |
|
IRF1 |
Interferon regulatory factor 1 |
A member of the interferon regulatory transcription factor family. An activator of interferon alpha and beta transcription |
Not DE |
10.01 |
9.74 |
|
NFKB2 |
Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) |
A pleiotropic transcription factor involved in inflammation, immunity, differentiation, cell growth and apoptosis |
5.35 |
8.68 |
5.76 |
|
TNF |
Tumor necrosis factor (TNF superfamily, member 2) |
A proinflammatory cytokine (secreted by macrophages) involved in the regulation cell proliferation, differentiation and apoptosis, and coagulation. |
15.16 |
80.07 |
15.00 |
|
AREGB |
Amphiregulin B |
A growth-modulating glycoprotein |
−3.84 |
−9.70 |
−5.09 |
|
FOS |
FBJ murine osteosarcoma viral oncogene homolog |
A leucine zipper protein member of the AP-1 transcription factor complex. |
−3.69 |
−5.50 |
−3.61 |
|
PIK3IP1 |
Phosphoinositide-3-kinase interacting protein 1 |
Suppresses the activity of phosphatidylinositol-3-kinase (PI3K), a regulator of cell division |
−2.06 |
−1.68 |
Not DE |
| SPRY2 | Sprouty homolog 2 (Drosophila) | An inhibitor of receptor tyrosine kinase signalling proteins | −2.12 | −4.64 | Not DE |
Geometric mean fold-changes of gene expression (M. bovis-infected samples relative to control samples) are given for the RNA-seq sense strand, microarray and real time qRT-PCR data. Unless specified, results for each gene using the three techniques displayed significant differential expression (P-value ≤ 0.05). ‘Not DE’ indicates that a gene was not differentially expressed.