Table 1.

Gene sets enriched in PBSC CD34+ cells from patients who later develop t-MDS/AML

Gene set	Training set		Test Set
	NES	FDR q-val	NES	FDR q-val
Enriched in Cases
G-Protein coupled receptors
HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION	2.83	<0.001	3.89	<0.001
GPCRDB_CLASS_A_RHODOPSIN_LIKE	2.60	<0.001	3.35	<0.001
GPCRS_CLASS_A_RHODOPSIN_LIKE	2.52	<0.001	2.83	<0.001
MONOAMINE_GPCRS	2.32	0.003	2.62	<0.001
PEPTIDE_GPCRS	2.21	0.005	2.86	<0.001
Hematopoietic regulation
HALMOS_CEBP_DN	2.33	0.003	1.73	0.079
HOX_GENES	1.89	0.036	1.06	0.738
HSA04340_HEDGEHOG_SIGNALING_PATHWAY	1.76	0.058	2.15	0.005
Cell adhesion/communication
HSA01430_CELL_COMMUNICATION	2.05	0.009	2.86	<0.001
CELL_ADHESION	1.63	0.108	1.82	0.061
Xenobiotic metabolism
GAMMA_HEXACHLOROCYCLOHEXANE_DEGRADATION	2.04	0.009	2.01	0.018
Enriched in controls (reduced in cases)
Mitochondria and oxidative phosphorylation
HUMAN_MITODB_6_2002	−2.92	<0.001	−3.93	<0.001
HSA00190_OXIDATIVE_PHOSPHORYLATION	−2.88	<0.001	−3.01	<0.001
ELECTRON_TRANSPORT_CHAIN	−2.85	<0.001	−3.17	<0.001
MITOCHONDRIA	−2.84	<0.001	−3.85	<0.001
MOOTHA_VOXPHOS	−2.74	<0.001	−3.08	<0.001
OXIDATIVE_PHOSPHORYLATION	−2.58	<0.001	−2.67	<0.001
Ribosomes
HSA03010_RIBOSOME	−3.02	<0.001	−4.06	<0.001
RIBOSOMAL_PROTEINS	−3.01	<0.001	−3.77	<0.001
tRNA biosynthesis
TRNA_SYNTHETASES	−2.68	<0.001	−2.71	<0.001
AMINOACYL_TRNA_BIOSYNTHESIS	−2.41	<0.001	−2.74	<0.001
HSA00970_AMINOACYL_TRNA_BIOSYNTHESIS	−2.27	<0.001	−2.76	<0.001
Proteasomal pathway
PROTEASOMEPATHWAY	−2.47	<0.001	−3.14	<0.001
HSA03050_PROTEASOME	−2.47	<0.001	−2.69	<0.001
PROTEASOME_DEGRADATION	−2.32	<0.001	−2.52	<0.001
Cell cycle regulation
DNA_REPLICATION_REACTOME	−2.37	<0.001	−2.64	<0.001
P21_P53_MIDDLE_DN	−2.26	<0.001	−1.45	0.107
P21_P53_ANY_DN	−2.16	6.79E-04	−2.33	<0.001
SERUM_FIBROBLAST_CELLCYCLE	−2.14	0.014456	−1.74	0.029
CELL_CYCLE_KEGG	−1.91	0.005942	−1.97	0.008
Metabolism
KREBS_TCA_CYCLE	−2.46	<0.001	−2.46	<0.001
HSA00020_CITRATE_CYCLE	−2.23	2.31E-04	−2.55	<0.001
PENG_LEUCINE_DN	−2.22	4.46E-04	−3.65	<0.001
HSA00252_ALANINE_AND_ASPARTATE_METABOLISM	−2.05	0.001727	−1.00	0.535
PROPANOATE_METABOLISM	−1.98	0.003869	−2.82	<0.001
Hematopoietic stem cells
HSC_INTERMEDIATEPROGENITORS_ADULT	−2.42	<0.001	−3.15	<0.001
HSC_LATEPROGENITORS_ADULT	−2.36	<0.001	−3.73	<0.001
HSC_INTERMEDIATEPROGENITORS_SHARED	−2.35	<0.001	−3.19	<0.001
HSC_LATEPROGENITORS_FETAL	−2.31	<0.001	−3.61	<0.001
HSC_LATEPROGENITORS_SHARED	−2.28	<0.001	−3.87	<0.001
DNA repair
BRENTANI_REPAIR	−2.23	<0.001	−1.68	0.039

See also Table S3