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Table 2 The 20 Most Significant Gene Sets from the ASD Dataset for Deletions

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

Gene Set Name nominal p-value FDR q-value Holm's p-value Overlap proportion
NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON 1.876E-05 0.061 0.061 0.051
PEREZ_TP53_TARGETS 9.768E-05 0.078 0.319 0.019
REACTOME_RNA_POLYMERASE_I_III_AND_MITOCHONDRIAL_TRANSCRIPTION 1.026E-04 0.078 0.336 0.092
ONKEN_UVEAL_MELANOMA_UP 1.065E-04 0.078 0.348 0.098
BROWNE_HCMV_INFECTION_24HR_DN 1.187E-04 0.078 0.388 0.065
REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE 1.490E-04 0.081 0.487 0.098
BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_UP 1.937E-04 0.091 0.633 0.052
STARK_HYPPOCAMPUS_22Q11_DELETION_DN 0.001 0.218 1.000 0.115
KEGG_GAP_JUNCTION 0.001 0.218 1.000 0.133
DAIRKEE_TERT_TARGETS_UP 0.001 0.218 1.000 0.111
BLALOCK_ALZHEIMERS_DISEASE_UP 0.001 0.229 1.000 0.062
RODWELL_AGING_KIDNEY_UP 0.001 0.229 1.000 0.067
WALLACE_PROSTATE_CANCER_RACE_UP 0.001 0.268 1.000 0.035
AMUNDSON_RESPONSE_TO_ARSENITE 0.001 0.284 1.000 0.105
NIKOLSKY_BREAST_CANCER_16P13_AMPLICON 0.001 0.284 1.000 0.050
CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP 0.001 0.284 1.000 0.039
FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN 0.001 0.284 1.000 0.123
IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP 0.002 0.327 1.000 0.045
BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP 0.002 0.341 1.000 0.057
HSIAO_HOUSEKEEPING_GENES 0.002 0.360 1.000 0.260
  1. This table lists the 20 most statistically significant gene sets as determined by a one-tailed Fisher's exact test, according to Pinto [12]. This analysis was based on the 2 × 2 contingency table shown in Table 3b. Multiple testing was adjusted using Benjamini-Hochberg and Holm's procedures. Results of unadjusted and adjusted tests (Benjamini-Hochberg and Holm's procedure) are referred to as nominal p-value, FDR q-value, and Holm's p-value, respectively. Overlap proportions with the gene cluster detected by the proposed test are referred to as overlap proportion.