Table 2.
Enriched pathways in cxcr4b −/− neutrophils (analysis performed with DESeq2 paired).
| DESEq2 paired | ||||
|---|---|---|---|---|
| Gene ID | Gene symbol | Gene name | LogFC | p |
| Focal adhesion/ECM-receptor interaction | ||||
| ENSDARG00000032639 | cd36 | CD36 molecule (thrombospondin receptor) | −1.3 | 8.3E-03 |
| ENSDARG00000012405 | col1a1a | collagen, type I, alpha 1a | 0.8 | 2.2E-02 |
| ENSDARG00000061436 | col6a2 | collagen, type VI, alpha 2 | 1.0 | 4.5E-02 |
| ENSDARG00000074316 | itga1 | integrin, alpha 1 | 1.1 | 8.8E-03 |
| ENSDARG00000103056 | itga4 | integrin alpha 4 | 0.8 | 2.6E-02 |
| ENSDARG00000020785 | lama4 | laminin, alpha 4 | 1.1 | 7.1E-03 |
| ENSDARG00000093572 | lamc3 | laminin, gamma 3 | 1.5 | 5.2E-03 |
| ENSDARG00000060711 | sv2bb | synaptic vesicle glycoprotein 2Bb | 1.7 | 3.4E-03 |
| ENSDARG00000008867 | rap1b | RAP1B, member of RAS oncogene family | −0.9 | 2.1E-02 |
| ENSDARG00000007825 | map2k1 | mitogen-activated protein kinase kinase 1 | −1.1 | 2.1E-02 |
| ENSDARG00000098578 | pdgfab | platelet-derived growth factor alpha polypeptide b | −1.0 | 2.1E-02 |
| Cardiac muscle contraction | ||||
| ENSDARG00000007739 | atp1a1a.2 | ATPase, Na+/K+ transporting, alpha 1a polypeptide | −1.6 | 5.8E-05 |
| ENSDARG00000018259 | atp1a3a | ATPase, Na+/K+ transporting, alpha 3a polypeptide | 0.9 | 9.6E-03 |
| ENSDARG00000076833 | atp1b1b | ATPase, Na+/K+ transporting, beta 1b polypeptide | −1.5 | 4.0E-04 |
| ENSDARG00000063905 | mt-co1 | cytochrome c oxidase I, mitochondrial | −0.7 | 9.3E-03 |
| ENSDARG00000063908 | mt-co2 | cytochrome c oxidase II, mitochondrial | −0.6 | 4.1E-02 |
| ENSDARG00000063911 | mt-atp6 | ATP synthase 6, mitochondrial | −0.7 | 2.0E-02 |
| ENSDARG00000063912 | mt-co3 | cytochrome c oxidase III, mitochondrial | −0.7 | 1.7E-02 |
| ENSDARG00000023886 | cacna2d4b | calcium channel, voltage-dependent, alpha 2/delta subunit 4b | 1.2 | 3.2E-02 |
| ENSDARG00000045230 | cox6b1 | cytochrome c oxidase subunit VIb polypeptide 1 | −1.2 | 4.2E-03 |
| ENSDARG00000038075 | cyc1 | cytochrome c-1 | −0.7 | 1.9E-02 |
| ENSDARG00000079564 | vmhc | ventricular myosin heavy chain | 2.1 | 3.7E-05 |
| Axon guidance | ||||
| ENSDARG00000044029 | efnb3a | ephrin-B3a | 1.2 | 3.2E-02 |
| MAPK signaling pathway | ||||
| ENSDARG00000008867 | rap1b | RAP1B, member of RAS oncogene family | −0.9 | 2.1E-02 |
| ENSDARG00000035535 | rasa1a | RAS p21 protein activator (GTPase activating protein) 1a | 0.8 | 4.5E-02 |
| ENSDARG00000005482 | rapgef2 | Rap guanine nucleotide exchange factor (GEF) 2 | 1.0 | 9.9E-03 |
| ENSDARG00000043241 | arrb1 | arrestin, beta 1 | 1.3 | 3.1E-02 |
| ENSDARG00000023886 | cacna2d4b | calcium channel, voltage-dependent, alpha 2/delta subunit 4b | 1.2 | 3.2E-02 |
| ENSDARG00000102474 | dusp16 | dual specificity phosphatase 16 | 1.4 | 9.6E-04 |
| ENSDARG00000061255 | dusp3a | dual specificity phosphatase 3a | 1.4 | 1.5E-02 |
| ENSDARG00000009299 | dusp8a | dual specificity phosphatase 8a | 1.0 | 3.0E-03 |
| ENSDARG00000092281 | FLNB | filamin B | 1.3 | 2.1E-02 |
| ENSDARG00000007825 | map2k1 | mitogen-activated protein kinase kinase 1 | −1.1 | 2.1E-02 |
| ENSDARG00000001234 | map4k2 | mitogen-activated protein kinase kinase kinase kinase 2 | −1.2 | 2.9E-02 |
| ENSDARG00000071357 | map4k3b | mitogen-activated protein kinase kinase kinase kinase 3b | 1.3 | 3.2E-03 |
| ENSDARG00000070454 | pla2g12a | phospholipase A2, group XIIA | −1.4 | 1.4E-02 |
| ENSDARG00000015662 | pla2g12b | phospholipase A2, group XIIB | −1.4 | 1.4E-02 |
| ENSDARG00000098578 | pdgfab | platelet-derived growth factor alpha polypeptide b | −1.0 | 2.1E-02 |
| ENSDARG00000060551 | rps6ka5 | ribosomal protein S6 kinase, polypeptide 5 | 1.5 | 8.7E-04 |
| ENSDARG00000017494 | tgfbr1a | transforming growth factor, beta receptor 1a | 1.2 | 4.1E-02 |
Pathway analysis in Cxcr4b-deficient neutrophils. Genes selected with DESeq (p < 0.05) and edgeR (p < 0.05) analyses in RStudio (from 21621 to 615 genes) were converted to the human orthologues using g:PROFILER and uploaded in DAVID Bioinformatics Resources 6.7 for pathway analysis. Up-regulation of genes involved in focal adhesion/ECM-Receptor interaction and axon guidance was identified, whereas down-regulation of genes in the metabolism of xenobiotic by P450 was found. Additional analysis was performed using DESeq2 paired (Table 2). The same pathways were identified with DESeq/edgeR (Table 1) and DESeq2 paired (Table 2) and the genes listed in Table 2 were in addition to genes described in Table 1. Enriched pathways indicate alteration in motility, as shown by the analysis performed with DESeq and edgeR and reveal members of the MAPK signaling to be differentially expressed.