A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data

BMC Bioinformatics

Table 1 Gene Sets Overlapping with the Detected Gene Cluster at a Proportion of ≥50%

Gene Set Name	Overlap Proportion	Gene Set Size
BIOCARTA_PROTEASOME_PATHWAY	0.63	19
REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1	0.58	48
REACTOME_P53_INDEPENDENT_DNA_DAMAGE_RESPONSE	0.58	43
NGO_MALIGNANT_GLIOMA_1P_LOH	0.57	7
REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION	0.57	58
REACTOME_SIGNALING_BY_WNT	0.57	58
REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION	0.57	23
REACTOME_SCF_SKP2_MEDIATED_DEGRADATION_OF_P27_P21	0.56	52
REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G	0.55	47
BIOCARTA_SRCRPTP_PATHWAY	0.55	11
BIOCARTA_SET_PATHWAY	0.55	11
REACTOME_STABILIZATION_OF_P53	0.54	46
IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN	0.54	13
REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE	0.53	47
KEGG_PROTEASOME	0.52	48
REACTOME_ORC1_REMOVAL_FROM_CHROMATIN	0.51	63
GILMORE_CORE_NFKB_PATHWAY	0.50	10
FIRESTEIN_CTNNB1_PATHWAY_AND_PROLIFERATION	0.50	8
KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_DN	0.50	6
BIOCARTA_CDMAC_PATHWAY	0.50	16
REACTOME_SHC_MEDIATED_SIGNALLING	0.50	12

This table lists the gene sets with an overlapping proportion ≥50% for the gene cluster detected by the proposed test. For this analysis, we used all 3272 curated gene sets in MsigDB (ver 3.0) [24].

ISSN: 1471-2105