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

Li, Ming D; Wang, Ju; Niu, Tianhua; Ma, Jennie Z; Seneviratne, Chamindi; Ait-Daoud, Nassima; Saadvandi, Jim; Morris, Rana; Weiss, David; Campbell, Jan; Haning, William; Mawhinney, David J; Weis, Denis; McCann, Michael; Stock, Christopher; Kahn, Roberta; Iturriaga, Erin; Yu, Elmer; Elkashef, Ahmed; Johnson, Bankole A

doi:10.1186/s12920-014-0065-x

Table 3 Significantly enriched pathways detected exclusively in week 8 and week 12 topiramate groups (n = 27)^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

	Week 8 TPM			Week 12 TPM
Pathway name ^b	No. genes	P Value	FDR ^c	No. genes	P Value	FDR ^c
Neuronal function / Synaptic plasticity ( n = 8 )
Alpha-adrenergic signaling^a	17	0.025	0.042	10	0.0036	0.029
Ephrin receptor signaling^a	36	1.70 × 10⁻⁴	7.18 × 10⁻⁴	17	5.75 × 10⁻⁴	0.0095
ErbB signaling pathway^b	18	0.0026	0.0081	8	0.0078	0.035
FGF signaling^a	18	0.0040	0.0086	8	0.017	0.074
GnRH signaling pathway^b	20	0.0017	0.0060	11	0.0012	0.013
mTOR signaling pathway^b	15	4.47 × 10⁻⁵	3.78 × 10⁻⁴	5	0.033	0.090
Neurotrophin/TRK signaling^a	17	9.33 × 10⁻⁴	0.0027	7	0.017	0.074
Synaptic long term Potentiation^a,b	29	6.17 × 10 ⁻⁶	7.44 × 10 ⁻⁵	10	0.012	0.058
Signal transduction ( n = 6 )
Adipocytokine signaling^b	14	0.0070	0.017	9	9.30 × 10⁻⁴	0.013
Fc Epsilon RI Signaling ^a,b	24	1.51 × 10 ⁻⁴	6.73 × 10 ⁻⁴	11	0.0018	0.021
LPS-stimulated MAPK signaling^a	23	2.75 × 10⁻⁶	4.65 × 10⁻⁵	9	0.0025	0.024
NF-κB signaling^a	33	3.02 × 10⁻⁵	2.04 × 10⁻⁴	14	0.0016	0.021
p38 MAPK signaling^a	20	0.0037	0.0082	9	0.014	0.062
SAPK/JNK signaling^a	18	0.011	0.021	14	1.35 × 10⁻⁵	5.56 × 10⁻⁴
Cardiovascular function ( n = 2 )
Cardiac hypertrophy signaling^a	42	2.45 × 10⁻⁴	9.22 × 10⁻⁴	16	0.013	0.062
Renin-angiotensin signaling^a	27	3.55 × 10⁻⁵	2.24 × 10⁻⁴	14	8.91 × 10⁻⁵	0.0025
Inflammation / Immune function ( n = 8 )
B cell activating factor signaling^a	10	0.013	0.023	5	0.022	0.090
CCR3 signaling in eosinophils^a	24	0.0013	0.0035	13	5.25 × 10⁻⁴	0.0095
CCR5 signaling in macrophages^a	13	0.030	0.048	11	5.62 × 10⁻⁵	0.0019
Chemokine signaling^a	21	4.37 × 10⁻⁵	2.54 × 10⁻⁴	8	0.0096	0.049
CXCR4 signaling^a	28	0.0065	0.014	11	0.045	0.14
Epithelial cell signaling in Helicobacter pylori infection^b	16	0.0011	0.0048	8	0.0063	0.031
Natural killer cell signaling ^a,b	26	1.15 × 10 ⁻⁴	5.54 × 10 ⁻⁴	12	0.0013	0.019
Role of PKR in Interferon Induction and Antiviral Response^a	11	0.0051	0.011	5	0.025	0.094
Other ( n = 3 )
Hepatic cholestasis^a	24	0.014	0.026	12	0.0076	0.042
Macropinocytosis^a	17	6.46 × 10⁻⁴	0.0021	8	0.0043	0.034
Xenobiotic metabolism signaling^a	37	0.044	0.065	19	0.0053	0.036

^aIngenuity Pathways Knowledge Base Pathways with Number of Genes ≥ 3, P Values < 0.05, FDRs < 0.05 at either Week 8 or Week 12 and FDRs < 0.10 at both were selected by Ingenuity Pathway Analysis (IPA) URL: http://www.ingenuity.com/.
^bKyoto Encyclopedia of Genes and Genomes (KEGG) pathways with Number of Genes ≥ 3 and Gamma P Values < 0.05, and FDRs < 0.05 at either Week 8 or Week 12 and FDRs < 0.10 at both were selected by Onto-Tools URL: http://vortex.cs.wayne.edu/ontoexpress/. For pathways identified by both IPA and Onto-Tools (shown in italic), only IPA results were presented.
^cFDR, denoting false discovery rate, was estimated by the Benjamini-Hochberg (BH) method.

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