Table 1 Enriched pathways in cxcr4b −/− neutrophils (analysis performed with DESeq and edgeR).

From: CXCR4 signaling regulates metastatic onset by controlling neutrophil motility and response to malignant cells

 

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

  1. 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.
  2. 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.
Back to article page