Transcriptional profiles of pilocytic astrocytoma are related to their three different locations, but not to radiological tumor features

Table 3 Selected gene sets differentiated between pilocytic astrocytomas of variable clinical features

Broad GeneSets	Number of genes	LS	KS	GSA
Broad GeneSets	Number of genes	p-value	p-value	p-value
KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3	100	0.00001	0.00001	<0.005
LI_CISPLATIN_RESISTANCE_UP	66	0.00001	0.00019	<0.005
REACTOME_ACTIVATED_TLR4_SIGNALLING	25	0.00001	0.00001	<0.005
REACTOME_TOLL_LIKE_RECEPTOR_4_CASCADE	28	0.00001	0.00001	<0.005
SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_DN	7	0.00001	0.00001	<0.005
SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_UP	31	0.00001	0.00001	<0.005
WATANABE_COLON_CANCER_MSI_VS_MSS_DN	96	0.00001	0.00041	<0.005
ZHAN_MULTIPLE_MYELOMA_PR_DN	69	0.00001	0.00001	<0.005
BIOCARTA_DC_PATHWAY	13	0.00023	0.00079	<0.005
CGGTGTG, MIR-220	8	0.00001	0.09215	<0.005
V$GNCF_01	93	0.00002	0.00239	0.04
GGGATGC, MIR-324-5P	72	0.00003	0.01085	<0.005
CCATCCA, MIR-432	64	0.00006	0.00044	0.015
V$POU3F2_01	94	0.00006	0.02333	0.025
CCANNAGRKGGC_UNKNOWN	89	0.00017	0.00001	0.035
V$CDPCR3_01	39	0.00028	0.02874	0.065
CCCACAT,MIR-299-3P	72	0.00034	0.08243	0.07
V$MYOGNF1_01	57	0.00045	0.01553	0.045
CTGYNNCTYTAA_UNKNOWN	73	0.00055	0.00747	0.09
GTACAGG, MIR-486	72	0.00056	0.00176	0.01
V$PAX8_01	49	0.00058	0.0018	<0.005
V$AHR_01	86	0.00068	0.05371	0.16
CCAATNNSNNNGCG_UNKNOWN	65	0.00407	0.22226	<0.005
AGTCTTA, MIR-499	99	0.02398	0.00033	0.22
V$MEF2_04	24	0.03997	0.01638	<0.005

Three independent tests: LS, KS permutation test, and Efron-Tibshirani’s GSA maxmean test were applied to select significantly affected gene classes

ISSN: 1471-2407