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Table 4 Top 50 significantly upregulated genes in RNA-seq and exon arrays

From: A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat

Gene symbol

Gene name

Rank RNA-seq

Rank exon arrays

Fold change RNA-seq

p adj RNA-seq

Fold change exon arrays

p adj exon arrays

Crisp3

Cysteine-rich secretory protein 1

1

5

1414.6

7.06E-10

21.0

2.58E-03

Csrp3

Cysteine and glycine-rich protein 3

2

3

590.1

4.30E-44

22.6

8.59E-05

Mmp12

Macrophage metaloelastase

3

14

427.5

2.98E-03

7.8

1.58E-02

Tgm1

Protein-glutamine gamma-glutamyltransferase k

4

25

355.1

2.18E-43

5.9

1.39 E-03

Hpd

4-hydroxyphenylpyruvate dioxygenase

5

34

237.3

1.56E-20

4.9

1.11E-03

Ucn

Urocortin

6

187

180.1

2.92E-36

2.5

1.10E-03

Sprr1a

Small proline-rich protein 1a / Cornifin-a

7

1

176.6

2.02E-25

57.9

2.36E-05

Serpina3n

Serine protease inhibitor A3N

8

4

174.6

1.97E-44

21.6

3.66E-04

Cxcl14

Chemokine (C-X-C motif) ligand 14

9

2

167.3

3.62E-08

33.4

1.59E-03

Hamp

Hepcidin antimicrobial peptide

10

11

162.5

5.41E-35

13.1

1.11E-03

Ptprh

Receptor-type tyrosine-protein phosphatase h

11

49

161.4

2.48E-48

3.9

1.40E-04

Rgd1305807 / LOC298077

Uncharacterized protein

12

2333

159.3

6.66E-06

1.2

1.89E-02

Cldn4

Claudin 4

13

31

159.2

3.29E-42

5.3

1.391E-03

Mmp7

Matrix metallopeptidase 7

14

319

158.3

2.62E-02

2.0

3.85E-02

Vip

Vasoactive intestinal peptide

15

28

138.2

3.21E-25

5.4

1.39E-03

Mroh4

Maestro heat-like repeat family member 4

16

ND

132.8

3.58E-08

-

-

Stac2

SH3 and cysteine-rich domain-containing protein 2

17

46

126.0

2.35E-69

4.1

1.43E-03

Ucn2

Urocortin 2

18

21

88.8

5.08E-04

6.0

2.67E-03

Il6

Interleukin 6

19

41

78.4

8.66E-18

4.5

1.58E-03

Serpinb2

Plasminogen activator inhibitor 2 type a

20

95

75.7

1.09E-34

3.2

6.07E-03

Abp1

Amiloride-sensitive amine oxidase

21

2050

73.8

6.06E-08

1.3

1.89E-02

D3zu79_rat/ lsmem1

Leucine rich single pass membrane protein

22

ND

73.7

8.13E-07

-

-

Ankrd1

Ankyrin repeat domain-containing protein 1

23

40

68.3

5.46E-31

4.5

2.22E-03

Cd8b

T-cell surface glycoprotein cd8 beta chain precursor

24

105

67.4

1.75E-02

3.0

1.24E-02

Vtcn1

V-set domain containing t cell activation inhibitor 1

25

183

67.4

1.13E-30

2.5

4.33 E-04

RT1-M2

RT1 class IB, locus M2

26

ND

64.9

2.54E-08

-

-

Il1a

Interleukin-1 alpha precursor

27

642

64.2

3.14E-22

1.7

5.58E-03

Reg3b

Regenerating islet-derived protein 3-beta

28

6

61.0

1.45E-114

20.1

2.36E-05

Il24

Interleukin-24

29

19

55.3

3.21E-25

6.4

1.39E-03

Igsf23

Immunoglobulin superfamily, member 23

30

ND

53.7

2.41E-28

-

-

En1

Homeobox protein engrailed

31

ND

51.6

2.90E-18

-

-

Trim55

Tripartite motif-containing protein 55

32

2142

49.4

1.24E-02

1.3

4.16E-02

Igsf7

Immunoglobulin superfamily, member 7

33

ND

46.9

1.51E-02

-

-

Cd8a

T-cell surface glycoprotein CD8 alpha chain

34

20

46.7

2.16E-03

6.1

4.13E-03

Gal

Galanin/GMAP prepropeptide

35

10

46.3

3.94E-58

13.5

1.36E-04

LOC363060/ Plet1

Placenta-induced transcript 1

36

588

41.2

5.17E-08

1.7

4.41E-03

Vsig4

V-set and immunoglobulin domain containing 4

37

1752

39.7

1.18E-02

1.3

5.80E-02

Nps

Neuropeptide S

38

ND

37.4

2.07E-07

-

-

Htr2b

5-hydroxytryptamine receptor 2b, g-protein coupled

39

18

36.3

8.44E-04

7.2

3.89E-03

Col7a1

Collagen alpha-1(VII) chain precursor

40

1426

34.2

2.37E-11

1.4

1.60E-02

Atf3

Activating transcription factor 3

41

9

33.8

2.36E-66

13.7

1.99E-05

Novel

Novel protein coding

42

ND

32.8

1.61E-03

-

-

Gpnmb

Transmembrane glycoprotein nmb

43

8

31.9

4.00E-03

14.3

1.39E-03

Lilrb4

Leukocyte immunoglobulin-like receptor, subfamily b, member 4

44

12

31.6

6.33E-02

9.1

3.14E-02

Gzmb

Granzyme b (granzyme 2, cytotoxic t-lymphocyte-associated serine esterase 1)

45

7

31.4

2.52E-11

16.6

4.87E-05

Arg1

Arginase-1

46

197

30.1

2.30E-66

2.4

2.00E-03

Fcrls

Fc receptor-like s, scavenger receptor

47

ND

30.0

7.34E-05

-

-

Mmp10

Matrix metallopeptidase 10

48

NS

29.2

4.47E-03

1.1

NS

Lce1f

Late cornified envelope 1F

49

ND

28.3

5.03E-04

-

-

Cnga4

Cyclic nucleotide gated channel alpha 4

50

NS

27.7

5.20E-12

1.1

NS

Npy

Neuropeptide Y

ND

13

-

-

7.8

4.12E-03

Cthrc1

Collagen triple helix repeat containing 1

90

15

16.9

4.57E-04

7.6

2.39E-03

Clec7a

C-type lectin domain family 7, member a

91

16

16.2

5.58E-04

7.4

3.61E-03

Cd68

Macrosialin precursor

71

17

21.8

4.51E-03

7.4

3.84E-03

Thbs2

Thrombospondin 2 precursor

87

22

17.3

1.66E-04

6.0

3.41E-03

Ccl9

Chemokine (C-C motif) ligand 9

55

23

25.3

8.48E-07

5.9

4.92E-03

Apobec1

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1

104

24

14.3

1.37E-04

5.9

4.62E-03

C1qb

Complement C1Q subcomponent subunit B precursor

160

26

10.1

2.82E-04

5.5

2.15E-03

Cdkn1a

Cyclin-dependent kinase inhibitor 1

174

27

9.6

1.20E-29

5.4

5.12E-04

Postn

Periostin precursor

132

29

11.3

1.33E-04

5.4

4.78E-03

Fcgr2a

Low affinity immunoglobulin gamma fc region receptor iii

ND

30

-

-

5.3

4.26E-03

Crlf1

Cytokine receptor-like factor 1

110

32

13.1

4.06E-04

5.1

4.22E-03

C1qa

Complement C1Q subcomponent subunitA

135

33

11.2

9.39E-05

5.0

1.43E-03

Trem2

Triggering receptor expressed on myeloid cells 2

68

35

22.3

2.64E-03

4.8

7.16E-03

Cxcl9

Chemokine (C-X-C motif) ligand 9

301

36

6.7

7.44E-09

4.6

5.39E-03

Socs3

Suppressor of cytokine signaling 3

239

37

7.7

1.66E-06

4.6

1.09E-02

Gadd45a

Growth arrest and DNA damage-inducible protein gadd45 alpha

287

38

6.8

5.03E-25

4.6

3.03E-04

C1qc

Complement c1q subcomponent subunit c

235

39

7.7

2.65E-04

4.5

2.99E-03

Ly49si2

Immunoreceptor ly49si2

ND

42

-

-

4.5

2.92E-02

RT1-DA

RT1 class II, locus Da

307

43

6.7

5.88E-17

4.3

2.45E-03

Tgfbr1

Transforming growth factor, beta receptor 1

528

44

4.6

5.23E-03

4.2

4.92E-03

Ecel1

Endothelin converting enzyme-like 1

51

45

27.0

1.52E-93

4.1

4.87E-05

Cx3cr1

Chemokine (C-X3-C motif) receptor 1

219

47

8.1

1.08E-05

3.9

3.40E-03

RT1-BB

RT1 class II, locus Bb beta chain

308

48

6.7

5.23E-06

3.9

1.76E-03

Cxcl10

Chemokine (C-X-C motif) ligand 10

251

50

7.5

5.36E-03

3.8

1.88E-02

  1. Rank indicates highest significant fold changes determined by each method in descending order. In order to obtain a numeric FC for genes with infinite fold changes, a read count of one was ascribed to the naïve samples.
  2. NS- Non significant; ND- not detectable by exon arrays due to lack of probes in the core or extended confidence level or not detectable by RNA-Seq due to the existence of paralogous rat genes sharing high sequence homology leading to reads being classified as ambiguous and discarded from the analysis.