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Table 1 A list of 48 representative genes significantly up-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
CD164 CD164 molecule, sialomucin 2.67 ± 0.38 1.00 × 10−6 5.07 × 10−5
ITGA4 Integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor) 2.24 ± 0.27 4.00 × 10−6 1.31 × 10−4
ITGB1 Integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) 2.20 ± 0.25 1.10 × 10−5 2.64 × 10−4
SCYL2 SCY1-like 2 (S. cerevisiae) 2.45 ± 0.30 4.00 × 10−6 1.31 × 10−4
Synaptic plasticity and nervous system development / function
DLG1 Discs, large homolog 1 (Drosophila) 1.66 ± 0.12 2.00 × 10−6 8.22 × 10−5
GDI2 GDP dissociation inhibitor 2 1.63 ± 0.09 <1.00 × 10−6 <1.00 × 10−5
HIF1A Hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) 2.22 ± 0.26 4.00 × 10−6 1.31 × 10−4
SCFD1 Sec1 family domain containing 1 1.63 ± 0.12 3.00 × 10−6 1.09 × 10−4
SNAP23 Synaptosomal-associated protein, 23kDa 1.95 ± 0.19 2.00 × 10−6 8.22 × 10−5
TRAK2 Trafficking protein, kinesin binding 2 1.44 ± 0.07 <1.00 × 10−6 <1.00 × 10−5
ZFR Zinc finger RNA binding protein 2.14 ± 0.22 1.00 × 10−6 5.07 × 10−5
Signal transduction
AKAP11 A kinase (PRKA) anchor protein 11 2.23 ± 0.29 1.10 × 10−5 2.60 × 10−4
CCNYL1 Cyclin Y-like 1 1.62 ± 0.10 3.00 × 10−6 1.09 × 10−4
ERBB2IP Erbb2 interacting protein 2.28 ± 0.23 <1.00 × 10−6 <1.00 × 10−5
FGFR1OP2 FGFR1 oncogene partner 2 1.57 ± 0.11 4.00 × 10−6 1.31 × 10−4
MAPK1IP1L Mitogen-activated protein kinase 1 interacting protein 1-like 1.39 ± 0.06 <1.00 × 10−6 <1.00 × 10−5
PIK3AP1 Phosphoinositide-3-kinase adaptor protein 1 1.70 ± 0.14 5.00 × 10−6 1.54 × 10−4
PIK3R1 Phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 2.04 ± 0.23 7.00 × 10−6 1.92 × 10−4
PIP5K3 Phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III 1.95 ± 0.20 1.00 × 10−5 2.53 × 10−4
PTEN Phosphatase and tensin homolog 2.01 ± 0.10 <1.00 × 10−6 <1.00 × 10−5
RABEP1 Rabaptin, RAB GTPase binding effector protein 1 1.42 ± 0.08 5.00 × 10−6 1.54 × 10−4
RAP2A RAP2A, member of RAS oncogene family 1.75 ± 0.15 8.00 × 10−6 2.13 × 10−4
RAP2C RAP2C, member of RAS oncogene family 1.84 ± 0.16 3.00 × 10−6 1.09 × 10−4
SKAP2 Src kinase associated phosphoprotein 2 1.76 ± 0.15 5.00 × 10−6 1.54 × 10−4
SOS2 Son of sevenless homolog 2 (Drosophila) 2.51 ± 0.25 <1.00 × 10−6 <1.00 × 10−5
TGFBR2 Transforming growth factor, beta receptor II (70/80kDa) 1.49 ± 0.09 8.00 × 10−6 2.13 × 10−4
TOB1 Transducer of ERBB2, 1 2.28 ± 0.27 1.00 × 10−6 5.07 × 10−5
ZFAND6 Zinc finger, AN1-type domain 6 2.25 ± 0.20 <1.00 × 10−6 <1.00 × 10−5
Ubiquitination/Intracellular protein transport
CUL5 Cullin 5 2.25 ± 0.29 6.00 × 10−6 1.72 × 10−4
FBXL5 F-box and leucine-rich repeat protein 5 1.69 ± 0.09 <1.00 × 10−6 <1.00 × 10−5
FBXO28 F-box protein 28 1.45 ± 0.08 5.00 × 10−6 1.54 × 10−4
PCNP PEST proteolytic signal containing nuclear protein 2.54 ± 0.35 3.00 × 10−6 1.09 × 10−4
PSMD12 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 1.77 ± 0.12 <1.00 × 10−6 <1.00 × 10−5
RNF11 Ring finger protein 11 3.29 ± 0.39 <1.00 × 10−6 <1.00 × 10−5
RNF149 Ring finger protein 149 1.51 ± 0.10 8.00 × 10−6 2.13 × 10−4
SEC62 SEC62 homolog (S. cerevisiae) 1.69 ± 0.12 <1.00 × 10−6 <1.00 × 10−5
SMURF2 SMAD specific E3 ubiquitin protein ligase 2 1.64 ± 0.10 <1.00 × 10−6 <1.00 × 10−5
SRP54 Signal recognition particle 54kDa 1.56 ± 0.10 3.00 × 10−6 1.09 × 10−4
UBE2D1 Ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast) 2.41 ± 0.30 2.00 × 10−6 8.22 × 10−5
XPO1 Exportin 1 (CRM1 homolog, yeast) 1.98 ± 0.18 <1.00 × 10−6 <1.00 × 10−5
YME1L1 YME1-like 1 (S. cerevisiae) 1.69 ± 0.11 <1.00 × 10−6 <1.00 × 10−5
Mitochondrial function / Metabolism and energy pathways
ATP8A1 ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 2.11 ± 0.24 9.00 × 10−6 2.38 × 10−4
GALNT7 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) 1.87 ± 0.17 3.00 × 10−6 1.09 × 10−4
MAN1A1 Mannosidase, alpha, class 1A, member 1 2.26 ± 0.28 6.00 × 10−6 1.72 × 10−4
NUDT5 Nudix (nucleoside diphosphate linked moiety X)-type motif 5 1.34 ± 0.04 <1.00 × 10−6 <1.00 × 10−5
PGK1 Phosphoglycerate kinase 1 1.35 ± 0.06 6.00 × 10−6 1.72 × 10−4
SLC25A46 Solute carrier family 25, member 46 2.20 ± 0.25 3.00 × 10−6 1.09 × 10−4
TXNL1 Thioredoxin-like 1 1.49 ± 0.08 1.00 × 10−6 5.07 × 10−5
  1. aGenes are selected from a total of 97 significantly up-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 reciprocal of 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.