Table 1 Overview of DE Mmp and Timp genes in the colon of MMP-9−/− and WT mice in control and DSS conditions.

From: Inhibition of gelatinase B/MMP-9 does not attenuate colitis in murine models of inflammatory bowel disease

Gene symbol

Gene name

DESeq

EdgeR

CuffDiff2

  

Log2 FC

Adj P value

Log2 FC

Adj P value

Log2 FC

Adj P value

MMP-9−/− control (n=8) versus WT control (n=8)

 Mmp9*

Matrix metalloproteinase 9

3.9

7.89 e-34

3.8

3.20 e-40

3.9

0.019

 Timp1

Tissue inhibitor of metalloproteinase 1

0.1

1

0.1

1

0.1

1

MMP-9−/− DSS (n=8) versus WT DSS (n=8)

 Mmp9*

Matrix metalloproteinase 9

−1.5

1

NA

NA

−1.3

0.999

 Timp1

Tissue inhibitor of metalloproteinase 1

0.8

1

0.78

1

0.8

0.999

WT DSS (n=8) versus WT control (n=8)

 Mmp2

Matrix metalloproteinase 2

1.3

0.052

1.3

1.44 e-04

1.3

8.31 e-04

 Mmp3

Matrix metalloproteinase 3

6.8

2.76 e-04

6.8

3.04 e-24

6.8

8.31 e-04

 Mmp7

Matrix metalloproteinase 7

2.5

0.014

2.4

6.70 e-05

2.4

0.077

 Mmp8†

Matrix metalloproteinase 8

NA

1.90 e-04

10.8

3.58 e-23

NA

8.31 e-04

 Mmp9

Matrix metalloproteinase 9

5.4

0.004

5.4

2.83 e-22

5.4

8.31 e-04

 Mmp10†

Matrix metalloproteinase 10

5.4

0.004

5.4

2.83 e-22

6.2

8.31 e-04

 Mmp12

Matrix metalloproteinase 12

6.2

4.05 e-05

6.2

1.89 e-24

2.0

8.31 e-04

 Mmp13

Matrix metalloproteinase 13

5.3

0.002

5.3

5.20 e-18

5.3

8.31 e-04

 Mmp19

Matrix metalloproteinase 19

2.3

0.019

2.3

4.07 e-06

2.3

0.005

 Timp1

Tissue inhibitor of metalloproteinase 1

5.5

1.57 e-04

5.6

1.41 e-22

5.6

8.31 e-04

MMP-9−/− DSS (n=8) versus MMP-9−/− control (n=8)

 Mmp2

Matrix metalloproteinase 2

4.2

0.368

2.1

1.45 e-04

2.1

0.018

 Mmp3

Matrix metalloproteinase 3

7.9

0.118

NA

NA

7.9

0.003

 Mmp7

Matrix metalloproteinase 7

3.5

0.031

3.5

5.44 e-06

3.5

0.325

 Mmp8†

Matrix metalloproteinase 8

11.9

9.37 e-06

10.6

1.17 e-23

11.9

0.009

 Mmp9*

Matrix metalloproteinase 9

1.05

1

NA

NA

0.2

0.871

 Mmp10†

Matrix metalloproteinase 10

8.0

0.005

8.0

1.95 e-20

8.0

7.61 e-04

 Mmp12

Matrix metalloproteinase 12

2.5

0.274

2.5

1.24 e-05

3.1

7.61 e-04

 Mmp13

Matrix metalloproteinase 13

6.8

0.055

6.8

1.31 e-16

6.8

7.61 e-04

 Mmp19

Matrix metalloproteinase 19

2.7

0.258

2.8

2.72 e-06

2.8

0.003

 Timp1

Tissue inhibitor of metalloproteinase 1

6.2

0.079

6.3

1.51 e-15

6.3

7.61 e-04

  1. adj, adjusted; DSS, dextran sodium sulphate; FC, fold change; NA, undetectable value.
  2. *In MMP-9−/− mice, reads were mapped only to exons 9–13 (non-functional read-through transcript containing the haemopexin domain), whereas no reads were mapped to exons 1–8 (the functional part of the Mmp9 gene). This explains the paradoxical difference between MMP-9−/− control and WT control mice.
  3. Gene symbols and names in bold represent significance regarding differential expression, bold gene symbols with a dagger (†) indicate overlap between significantly DE genes.
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