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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.