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Table 2 A List of 45 representative genes significantly down-regulated in week 8 topiramate group a

From: Transcriptome profiling and pathway analysis of genes expressed differentially in participants with or without a positive response to topiramate treatment for methamphetamine addiction

Gene symbol Gene name Week 8 TPM
   FC ± SD b P Value c FDR d
Cell adhesion / Motion
CDC2L2 Cell division cycle 2-like 2 −1.39 ± 0.07 1.10 × 10−5 2.64 × 10−4
CDC42EP2 CDC42 effector protein (Rho GTPase binding) 2 −2.01 ± 0.19 1.00 × 10−6 5.07 × 10−5
EMILIN2 Elastin microfibril interfacer 2 −1.41 ± 0.05 <1.00 × 10−6 <1.00 × 10−5
JAK3 Janus kinase 3 (a protein tyrosine kinase, leukocyte) −1.68 ± 0.11 1.00 × 10−6 5.07 × 10−5
TUBB2C Tubulin, beta 2C −1.39 ± 0.06 2.00 × 10−6 8.22 × 10−5
Nervous system development and function / synaptic plasticity
ADAT1 Adenosine deaminase, tRNA-specific 1 −1.61 ± 0.08 <1.00 × 10−6 <1.00 × 10−5
CIRBP Cold inducible RNA binding protein −1.74 ± 0.13 1.00 × 10−6 5.07 × 10−5
DGCR14 3-phosphoinositide dependent protein kinase-1 −1.45 ± 0.04 <1.00 × 10−6 <1.00 × 10−5
FKBP4 FK506 binding protein 4, 59 kDa −1.49 ± 0.10 6.00 × 10−6 1.72 × 10−4
NAPA N-ethylmaleimide-sensitive factor attachment protein, alpha −2.04 ± 0.21 1.00 × 10−6 5.07 × 10−5
P2RX1 Purinergic receptor P2X, ligand-gated ion channel, 1 −1.72 ± 0.13 2.00 × 10−6 8.22 × 10−5
PRKACA Solute carrier family 1 (glial high affinity glutamate transporter), member 3 −1.69 ± 0.15 1.10 × 10−5 2.64 × 10−4
SHC1 SHC (Src homology 2 domain containing) transforming protein 1 −1.23 ± 0.04 3.00 × 10−6 1.09 × 10−4
TRIM8 Tripartite motif-containing 8 −1.45 ± 0.06 4.00 × 10−6 1.31 × 10−4
Signaling transduction
ARHGEF2 Rho/rac guanine nucleotide exchange factor (GEF) 2 −1.62 ± 0.11 2.00 × 10−6 8.22 × 10−5
BCR Breakpoint cluster region −1.43 ± 0.06 <1.00 × 10−6 <1.00 × 10−5
GRINA Glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 −2.49 ± 0.28 <1.00 × 10−6 <1.00 × 10−5
LIMK2 LIM domain kinase 2 −3.05 ± 0.44 4.00 × 10−6 1.31 × 10−4
PHPT1 Phosphohistidine phosphatase 1 −1.33 ± 0.06 7.00 × 10−6 1.92 × 10−4
PLCB2 Phospholipase C, beta 2 −1.93 ± 0.13 <1.00 × 10−6 <1.00 × 10−5
RHOT2 Ras homolog gene family, member T2 −1.46 ± 0.05 <1.00 × 10−6 <1.00 × 10−5
Ubiquitination / Intracellular protein transport
AP2A1 Adaptor-related protein complex 2, alpha 1 subunit −2.04 ± 0.20 1.10 × 10−5 2.64 × 10−4
NPEPL1 Aminopeptidase-like 1 −1.26 ± 0.03 <1.00 × 10−6 <1.00 × 10−5
SHARPIN SHANK-associated RH domain interactor −2.13 ± 0.26 1.00 × 10−5 2.53 × 10−4
TRAPPC5 Trafficking protein particle complex 5 −1.58 ± 0.11 6.00 × 10−6 1.72 × 10−4
UBE2M Ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast) −1.70 ± 0.12 1.00 × 10−6 5.07 × 10−5
UBXN6 UBX domain protein 6 −2.40 ± 0.29 2.00 × 10−6 8.22 × 10−5
USP4 Ubiquitin specific peptidase 4 (proto-oncogene) −1.46 ± 0.06 2.00 × 10−6 8.22 × 10−5
WBP2 WW domain binding protein 2 −1.85 ± 0.18 4.00 × 10−6 1.31 × 10−4
Mitochondrial function / metabolism and energy pathways
ATAD3B ATPase family, AAA domain containing 3B −1.47 ± 0.07 <1.00 × 10−6 <1.00 × 10−5
B4GALT3 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3 −1.26 ± 0.04 1.00 × 10−6 5.07 × 10−5
COASY Coenzyme A synthase −1.29 ± 0.06 1.20 × 10−5 2.79 × 10−4
COX5B Cytochrome c oxidase subunit Vb −1.44 ± 0.09 1.20 × 10−5 2.79 × 10−4
GANAB Glucosidase, alpha; neutral AB −1.63 ± 0.08 <1.00 × 10−6 <1.00 × 10−5
MRPL37 Mitochondrial ribosomal protein L37 −1.30 ± 0.04 <1.00 × 10−6 <1.00 × 10−5
NAGK N-acetylglucosamine kinase −1.30 ± 0.05 4.00 × 10−6 1.31 × 10−4
NDUFV3 NADH dehydrogenase (ubiquinone) flavoprotein 3, 10 kDa −1.63 ± 0.08 <1.00 × 10−6 <1.00 × 10−5
PFKL Phosphofructokinase, liver −1.53 ± 0.10 3.00 × 10−6 1.09 × 10−4
UROD Uroporphyrinogen decarboxylase −1.35 ± 0.06 5.00 × 10−6 1.54 × 10−4
Immune system function
CISH Cytokine inducible SH2-containing protein −1.34 ± 0.05 1.00 × 10−6 5.07 × 10−5
HLA-E Major histocompatibility complex, class I, E −1.25 ± 0.04 <1.00 × 10−6 <1.00 × 10−5
JMJD3 Jumonji domain containing 3, histone lysine demethylase −2.03 ± 0.16 <1.00 × 10−6 <1.00 × 10−5
MSRB2 Methionine sulfoxide reductase B2 −1.68 ± 0.13 2.00 × 10−6 8.22 × 10−5
OAS1 2′,5′-oligoadenylate synthetase 1, 40/46 kDa −1.84 ± 0.15 1.00 × 10−6 5.07 × 10−5
TAPBP TAP binding protein (tapasin) −1.60 ± 0.06 <1.00 × 10−6 <1.00 × 10−5
  1. aGenes are selected from a total of 62 down-regulated genes with Bonferroni-corrected P Values < 0.05 (i.e., 0.05/3698 genes = 1.35 × 10−5).
  2. bFC, denoting fold change, is defined as the ratio of the expression values of Positive Responders over Negative Responders; SD, standard deviation.
  3. cP Value was calculated using the ordinary Student’s t test for each gene.
  4. dFDR, denoting false discovery rate, was estimated by the Benjamini-Hochberg (BH) method.