Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods

Morrow, Jarrett D; Qiu, Weiliang; Chhabra, Divya; Rennard, Stephen I; Belloni, Paula; Belousov, Anton; Pillai, Sreekumar G; Hersh, Craig P

doi:10.1186/s12920-014-0072-y

BMC Medical Genomics

Table 4 GSEA results for modules associated with exacerbations phenotypes (gene sets with FDR q-value < 0.25 are shown and viral response gene sets are in bold)

From: Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods

Module name	Gene set description	ID	Set overlap	P-value	FDR q-value
White (negative)*	NAIVE_BCELL_VS_MONOCYTE_UP	GSE22886	15	0.084	0.207
	CD4_TCELL_VS_BCELL_DN	GSE10325	18	0.122	0.230
	BCELL_VS_MONOCYTE_DAY7_FLU_VACCINE_P	GSE29618	17	0.185	0.216
Royalblue (positive)*	NAIVE_VS_PD1LOW_CD8_TCELL_DN	GSE26495	28	0.004	0.048
	HEALTHY_VS_RSV_INF_INFANT_PBMC_UP	GSE34205	15	0.016	0.062
	DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN		18	0.055	0.151
Lightgreen (negative)*	BCELL_VS_MDC_DAY7_FLU_VACCINE_UP	GSE29618	17	0.006	0.095
	CD4_TCELL_VS_BCELL_DN	GSE10325	19	0.012	0.05
	BCELL_VS_MDC_UP	GSE29618	15	0.012	0.043
	LUPUS_CD4_TCELL_VS_LUPUS_BCELL_DN	GSE10325	20	0.01	0.046
	DODD_NASOPHARYNGEAL_CARCINOMA_UP		15	0.023	0.068
	BCELL_VS_MONOCYTE_DAY7_FLU_VACCINE_UP	GSE29618	21	0.025	0.064
	BCELL_VS_MYELOID_UP	GSE10325	15	0.045	0.064
	NAIVE_BCELL_VS_MONOCYTE_UP	GSE22886	17	0.06	0.078
	BCELL_VS_MONOCYTE_UP	GSE29618	23	0.075	0.121
	CAGGTG_V$E12_Q6		16	0.116	0.149
	MEMORY_CD4_TCELL_VS_BCELL_DN	GSE3982	17	0.137	0.14
Darkturquoise (positive)*	NAIVE_VS_PD1LOW_CD8_TCELL_DN	GSE26495	26	0.057	0.090
Darkturquoise (positive)*	NAIVE_VS_PD1HIGH_CD8_TCELL_DN	GSE26495	19	0.158	0.166
Darkgrey (positive)*	CTRL_VS_NEWCASTLE_VIRUS_DC_8H_DN	GSE18791	30	0.000	0.012
	BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE		18	0.003	0.038
	UNSTIM_VS_4H_LPS_DC_TRANSLATED_RNA_DN	GSE14000	23	0.002	0.030
	MOSERLE_IFNA_RESPONSE		17	0.011	0.104
	TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP		20	0.016	0.094
	UNSTIM_VS_NEWCATSLE_VIRUS_DC_18H_DN	GSE18791	19	0.013	0.093
	UNSTIM_VS_NEWCATSLE_VIRUS_DC_6H_DN	GSE18791	31	0.031	0.105
	CTRL_VS_NEWCASTLE_VIRUS_DC_10H_DN	GSE18791	21	0.013	0.095
	CTRL_VS_NEWCASTLE_VIRUS_DC_12H_DN	GSE18791	19	0.026	0.134
	UNSTIM_VS_4H_LPS_DC_DN	GSE14000	24	0.031	0.141
	UNSTIM_VS_NEWCATSLE_VIRUS_DC_10H_DN	GSE18791	26	0.034	0.161
	CTRL_VS_NEWCASTLE_VIRUS_DC_4H_DN	GSE18791	22	0.052	0.166
	CTRL_VS_NEWCASTLE_VIRUS_DC_6H_DN	GSE18791	27	0.054	0.170
	BCELL_VS_LUPUS_BCELL_DN	GSE10325	17	0.094	0.250
	HECKER_IFNB1_TARGETS		21	0.102	0.246

*Positive or negative correlation between module and phenotype.

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ISSN: 1755-8794

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