Table 1.
Enriched pathways in cxcr4b −/− neutrophils (analysis performed with DESeq and edgeR).
| DESEq | edgeR | |||||
|---|---|---|---|---|---|---|
| Gene ID | Gene symbol | Gene name | LogFC | p | LogFC | p |
| Focal adhesion/ECM-receptor interaction | ||||||
| ENSDARG00000056624 | figf | c-fos induced growth factor | 3.9 | 3.0E-02 | 3.9 | 3.0E-02 |
| ENSDARG00000009014 | col11a1b | collagen, type XI, alpha 1b | 1.8 | 6.0E-03 | 1.8 | 5.0E-03 |
| ENSDARG00000019815 | fn1a | fibronectin 1a | 1.9 | 3.0E-02 | 1.9 | 3.0E-02 |
| ENSDARG00000007950 | itga11b | integrin, alpha 11b | 4.8 | 3.0E-03 | 4.6 | 3.0E-03 |
| ENSDARG00000053232 | itgb1b.1 | integrin beta 1b.1 | 1.2 | 4.0E-02 | 1.2 | 4.0E-02 |
| ENSDARG00000102277 | lama1 | laminin, alpha 1 | 3.1 | 9.0E-03 | 3.1 | 1.0E-02 |
| ENSDARG00000099390 | lama2 | laminin, alpha 2 | 4 | 1.0E-02 | 3.9 | 2.0E-02 |
| ENSDARG00000018110 | pak4 | p21 protein (Cdc42/Rac)-activated kinase 4 | 1.5 | 2.0E-02 | 1.5 | 1.0E-02 |
| ENSDARG00000038139 | pdgfbb | platelet-derived growth factor beta polypeptide b | 6.8 | 8.0E-04 | 6.3 | 6.0E-03 |
| ENSDARG00000078362 | tnc | tenascin C | 1.6 | 2.0E-02 | 1.6 | 3.0E-02 |
| Axon guidance | ||||||
| ENSDARG00000007461 | srgap1 | SLIT-ROBO Rho GTPase activating protein 1 | 2.9 | 4.0E-02 | 2.9 | 4.0E-02 |
| ENSDARG00000045064 | ablim1b | actin binding LIM protein 1b | 1.3 | 2.0E-02 | 1.3 | 2.0E-02 |
| ENSDARG00000089790 | efna5a | ephrin-A5a | 2.8 | 1.0E-02 | 2.8 | 3.0E-02 |
| ENSDARG00000053232 | itgb1b.1 | integrin beta 1b.1 | 1.2 | 4.0E-02 | 1.2 | 4.0E-02 |
| ENSDARG00000022531 | ntn1b | netrin 1b | 2.6 | 9.0E-05 | 2.6 | 7.0E-03 |
| ENSDARG00000102556 | nfat5b | nuclear factor of activated T-cells 5 | 3.6 | 1.0E-02 | 3.5 | 2.6E-02 |
| ENSDARG00000076297 | nfatc3a | nuclear factor of activated T-cells, cytoplasmic 3a | 1.6 | 2.6E-02 | 1.6 | 3.2E-02 |
| ENSDARG00000018110 | pak4 | p21 protein (Cdc42/Rac)-activated kinase 4 | 1.5 | 2.2E-02 | 1.5 | 1.1E-02 |
| ENSDARG00000035132 | rgs3b | regulator of G-protein signaling 3b | 2.3 | 3.0E-03 | 2.3 | 5.0E-03 |
| ENSDARG00000088143 | sema4gb | semaphorin 4gb | 1.00E + 06 | 5.9E-04 | 7.9 | 4.5E-04 |
| ENSDARG00000099446 | slit1b | slit homolog 1b | 3.5 | 6.6E-03 | 3.5 | 2.3E-02 |
| Metabolism of xenobiotics by cytochrome P450 | ||||||
| ENSDARG00000006220 | ugt1ab | UDP glucuronosyltransferase 1 family a, b | −2.6 | 4.9E-05 | −2.6 | 8.2E-03 |
| ENSDARG00000091211 | adh8a | alcohol dehydrogenase 8a | −4.3 | 5.9E-03 | −4.2 | 4.6E-03 |
| ENSDARG00000098315 | cyp1a | cytochrome P450, family 1, subfamily A | −4.1 | 1.1E-10 | −4.1 | 4.0E-03 |
| ENSDARG00000101423 | cyp2y3 | cytochrome P450, family 2, subfamily Y, polypeptide 3 | −1.5 | 1.8E-02 | −1.5 | 4.7E-02 |
| ENSDARG00000103295 | cyp3a65 | cytochrome P450, family 3, subfamily A, polypeptide 65 | −2.7 | 3.3E-06 | −2.7 | 4.5E-02 |
| ENSDARG00000039832 | zgc:173961 | zgc:173961 | −2.6 | 1.4E-05 | −2.6 | 1.0E-02 |
| ENSDARG00000090228 | gstal | glutathione S-transferase | −2.7 | 1.1E-05 | −2.7 | 8.7E-03 |
| ENSDARG00000017388 | gstt1b | glutathione S-transferase theta 1b | −2.8 | 1.9E-03 | −2.8 | 8.4E-03 |
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/ECMReceptor 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.