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Table 2 P-values for top 30 gene sets discovered by the integrative method using the self-contained gene sets test

From: Integrating diverse genomic data using gene sets

Pathway E1 E2 C1 C2 INT INT for validation set
HSA04810_REGULATION_OF_ACTIN_CYTOSKELETON 0.0697 0.2250 < 10-4 < 10-4 < 10-4 0.0001
HSA04010_MAPK_SIGNALING_PATHWAY 0.1302 0.0746 < 10-4 < 10-4 < 10-4 < 10-4
HSA04060_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 0.1422 0.0132 < 10-4 < 10-4 < 10-4 0.0147
HSA04310_WNT_SIGNALING_PATHWAY 0.2389 0.0039 < 10-4 < 10-4 < 10-4 0.0001
HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION 0.1164 0.8695 0.0001 0.0005 < 10-4 0.0042
HSA00230_PURINE_METABOLISM 0.0034 0.0503 0.0000 0.0003 < 10-4 0.0022
TRANSLATION_FACTORS 0.0208 0.0155 0.0022 0.0052 0.0001 0.2711
HSA01030_GLYCAN_STRUCTURES_BIOSYNTHESIS_1 0.0781 0.0292 0.0004 0.0003 0.0001 0.0454
HSA04360_AXON_GUIDANCE 0.4293 0.1803 < 10-4 0.0106 0.0001 0.0001
GLUCONEOGENESIS* 0.0435 0.1010 0.0613 0.0106 0.0001 0.0409
GLYCOLYSIS* 0.0435 0.1010 0.0613 0.1065 0.0001 0.0409
HSA00500_STARCH_AND_SUCROSE_METABOLISM* 0.0448 0.2669 0.0140 0.0043 0.0001 0.0364
HSA04630_JAK_STAT_SIGNALING_PATHWAY 0.2975 0.0090 0.0022 0.0041 0.0002 0.0141
HSA04510_FOCAL_ADHESION 0.0423 0.0926 0.0042 0.0374 0.0002 10-4
MRNA_PROCESSING_REACTOME 0.1660 0.0062 0.0537 0.0004 0.0003 < 10-4
HSA05215_PROSTATE_CANCER 0.0534 0.3618 0.0013 0.0534 0.0004 0.0008
HSA01031_GLYCAN_STRUCTURES_BIOSYNTHESIS_2 0.0084 0.0076 0.0312 0.0141 0.0004 0.0926
HSA00240_PYRIMIDINE_METABOLISM 0.0013 0.0307 0.0022 0.0065 0.0004 0.0063
HSA04210_APOPTOSIS 0.1207 0.2064 0.0003 0.0001 0.0004 0.0021
HSA04620_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY 0.1986 0.1228 0.0001 0.0109 0.0004 0.0006
GLYCOLYSIS_AND_GLUCONEOGENESIS* 0.0209 0.1407 0.0476 0.0112 0.0005 0.1808
HSA04660_T_CELL_RECEPTOR_SIGNALING_PATHWAY 0.0192 0.1176 0.0141 0.0027 0.0006 0.0661
HSA00051_FRUCTOSE_AND_MANNOSE_METABOLISM* 0.1565 0.2238 0.0314 0.0112 0.0006 0.2631
HSA00010_GLYCOLYSIS_AND_GLUCONEOGENESIS* 0.0515 0.1333 0.1276 0.0148 0.0007 0.0647
INTEGRIN_MEDIATED_CELL_ADHESION_KEGG 0.2779 0.1734 0.0017 0.0038 0.0007 0.0001
HSA04640_HEMATOPOIETIC_CELL_LINEAGE 0.0634 0.0676 0.0140 0.0009 0.0007 0.0026
GPCRDB_CLASS_A_RHODOPSIN_LIKE 0.3429 0.4710 0.0003 0.0483 0.0008 0.0449
HSA00350_TYROSINE_METABOLISM 0.0219 0.0421 0.0772 0.0085 0.0008 0.0648
HSA05221_ACUTE_MYELOID_LEUKEMIA 0.0697 0.3196 0.0213 0.0105 0.0009 0.0310
CALCINEURIN_NF_AT_SIGNALING 0.1302 0.1298 0.0205 0.0005 0.0010 0.1128
  1. Asterisks indicate sets related to sugar metabolic processes. E1 and E2, single data type analysis using expression data; C1 and C2, single data type analysis using copy number data; INT, integrative method.