Thol et al. MEBE score in MDS – supplemental data

Table S6. List of gene sets enriched or depleted in MDS patients with high MEBE expression score.

Enriched gene sets in patients with high MEBE score
Gene set / Database / # genes in gene set / ES* / NES§ / NOM p-value
SH3_SH2_ADAPTOR_ACTIVITY / GO / 42 / 0.50 / 1.89 / 0.008
IL7PATHWAY / Biocarta / 16 / 0.73 / 1.86 / 0.002
APOPTOSIS_KEGG / Genmapp / 49 / 0.49 / 1.86 / 0.004
VIPPATHWAY / Biocarta / 27 / 0.51 / 1.83 / 0.010
MOLECULAR_ADAPTOR_ACTIVITY / GO / 48 / 0.48 / 1.81 / 0.008
ACUTE_MYELOID_LEUKEMIA_HSA05221 / Kegg / 53 / 0.49 / 1.81 / 0.002
TRANSCRIPTION_COREPRESSOR_ACTIVITY / GO / 85 / 0.40 / 1.77 / 0.010
NO2IL12PATHWAY / Biocarta / 15 / 0.80 / 1.77 / 0.012
IL12PATHWAY / Biocarta / 20 / 0.71 / 1.77 / 0.010
ANTIGEN_PROCESSING_AND_PRESENTATION_HSA04612 / Kegg / 75 / 0.52 / 1.77 / 0.024
TRANSCRIPTION_REPRESSOR_ACTIVITY / GO / 140 / 0.35 / 1.76 / 0.006
DEATHPATHWAY / Biocarta / 33 / 0.62 / 1.76 / 0.012
PROTEIN_KINASE_CASCADE / GO / 282 / 0.34 / 1.72 / 0.006
TCRPATHWAY / Biocarta / 44 / 0.58 / 1.71 / 0.017
T_CELL_RECEPTOR_SIGNALING_PATHWAY_HSA04660 / Kegg / 93 / 0.47 / 1.70 / 0.050
MEF2DPATHWAY / Biocarta / 20 / 0.51 / 1.70 / 0.023
PROTEIN_BINDING__BRIDGING / GO / 58 / 0.42 / 1.70 / 0.015
PROGRAMMED_CELL_DEATH / GO / 404 / 0.35 / 1.69 / 0.008
REGULATION_OF_PROGRAMMED_CELL_DEATH / GO / 318 / 0.37 / 1.68 / 0.002
APOPTOSIS_GO / GO / 403 / 0.35 / 1.68 / 0.008
REGULATION_OF_APOPTOSIS / GO / 317 / 0.36 / 1.68 / 0.002
APOPTOSIS_HSA04210 / Kegg / 83 / 0.46 / 1.68 / 0.022
JAK_STAT_CASCADE / GO / 30 / 0.47 / 1.67 / 0.021
IL2PATHWAY / Biocarta / 22 / 0.56 / 1.67 / 0.008
IL2RBPATHWAY / Biocarta / 34 / 0.48 / 1.66 / 0.029
CXCR4PATHWAY / Biocarta / 24 / 0.48 / 1.66 / 0.042
NOTCH_SIGNALING_PATHWAY_HSA04330 / Kegg / 43 / 0.40 / 1.66 / 0.012
NEGATIVE_REGULATION_OF_CELLULAR_PROTEIN_METABOLIC_PROCESS / GO / 42 / 0.50 / 1.65 / 0.033
S_ADENOSYLMETHIONINE_DEPENDENT_METHYLTRANSFERASE_ACTIVITY / GO / 22 / 0.52 / 1.65 / 0.032
NEGATIVE_REGULATION_OF_TRANSLATION / GO / 20 / 0.58 / 1.64 / 0.049
NEGATIVE_REGULATION_OF_BINDING / GO / 17 / 0.53 / 1.64 / 0.020
CCR5PATHWAY / Biocarta / 17 / 0.56 / 1.64 / 0.057
NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS / GO / 45 / 0.47 / 1.63 / 0.033
NEGATIVE_REGULATION_OF_PROGRAMMED_CELL_DEATH / GO / 141 / 0.37 / 1.63 / 0.010
APOPTOSIS / Genmapp / 67 / 0.52 / 1.62 / 0.023
NEGATIVE_REGULATION_OF_TRANSCRIPTION / GO / 171 / 0.32 / 1.62 / 0.004
NEGATIVE_REGULATION_OF_APOPTOSIS / GO / 140 / 0.36 / 1.62 / 0.010
AMIPATHWAY / Biocarta / 22 / 0.62 / 1.61 / 0.075
CSKPATHWAY / Biocarta / 22 / 0.62 / 1.61 / 0.075
MAPKKK_CASCADE_GO_0000165 / GO / 100 / 0.38 / 1.61 / 0.012
Depleted gene sets in patients with high MEBE score
Gene set / Database / # genes in gene set / ES* / NES§ / p-value
MICROSOME / GO / 42 / -0.53 / -1.88 / 0.002
VESICULAR_FRACTION / GO / 44 / -0.51 / -1.83 / 0.002
GALACTOSYLTRANSFERASE_ACTIVITY / GO / 16 / -0.57 / -1.82 / 0.000
INTRAMOLECULAR_OXIDOREDUCTASE_ACTIVITY / GO / 20 / -0.56 / -1.77 / 0.012
GLYCOPROTEIN_BIOSYNTHETIC_PROCESS / GO / 72 / -0.41 / -1.76 / 0.002
UDP_GLYCOSYLTRANSFERASE_ACTIVITY / GO / 39 / -0.44 / -1.68 / 0.008
RESPIRATORY_GASEOUS_EXCHANGE / GO / 15 / -0.64 / -1.67 / 0.006
ACTIN_FILAMENT / GO / 16 / -0.59 / -1.61 / 0.008
TRANSFERASE_ACTIVITY__TRANSFERRING_GROUPS_OTHER_THAN_AMINO_ACYL_GROUPS / GO / 47 / -0.33 / -1.60 / 0.013
TRANSFERASE_ACTIVITY__TRANSFERRING_HEXOSYL_GROUPS / GO / 78 / -0.36 / -1.60 / 0.014
PROTEIN_AMINO_ACID_N_LINKED_GLYCOSYLATION / GO / 29 / -0.46 / -1.57 / 0.013
BIOGENIC_AMINE_METABOLIC_PROCESS / GO / 17 / -0.56 / -1.57 / 0.031
GLYCOPROTEIN_METABOLIC_PROCESS / GO / 87 / -0.34 / -1.56 / 0.006
TRANSFERASE_ACTIVITY__TRANSFERRING_GLYCOSYL_GROUPS / GO / 107 / -0.33 / -1.56 / 0.014
AROMATIC_COMPOUND_METABOLIC_PROCESS / GO / 26 / -0.46 / -1.52 / 0.036
AMINE_CATABOLIC_PROCESS / GO / 25 / -0.45 / -1.52 / 0.045
NITROGEN_COMPOUND_CATABOLIC_PROCESS / GO / 27 / -0.45 / -1.50 / 0.053
CARBOHYDRATE_BIOSYNTHETIC_PROCESS / GO / 47 / -0.43 / -1.50 / 0.006
AMINO_ACID_CATABOLIC_PROCESS / GO / 23 / -0.47 / -1.50 / 0.064
N_ACYLTRANSFERASE_ACTIVITY / GO / 24 / -0.35 / -1.48 / 0.049
TRANSFERASE_ACTIVITY__TRANSFERRING_ACYL_GROUPS / GO / 57 / -0.30 / -1.48 / 0.020
LIPASE_ACTIVITY / GO / 48 / -0.55 / -1.47 / 0.014
REGULATION_OF_CELL_MIGRATION / GO / 27 / -0.54 / -1.47 / 0.023
TISSUE_REMODELING / GO / 29 / -0.53 / -1.45 / 0.020
AMINO_ACID_DERIVATIVE_METABOLIC_PROCESS / GO / 24 / -0.47 / -1.45 / 0.094
REGULATION_OF_CELL_MORPHOGENESIS / GO / 15 / -0.49 / -1.45 / 0.088
COLLAGEN / GO / 23 / -0.66 / -1.44 / 0.056
BONE_REMODELING / GO / 28 / -0.52 / -1.44 / 0.024
PHOSPHOLIPASE_ACTIVITY / GO / 40 / -0.49 / -1.44 / 0.044
CELL_CORTEX_PART / GO / 23 / -0.39 / -1.43 / 0.095
CELL_DIVISION / GO / 20 / -0.43 / -1.43 / 0.085
CARBOXYLESTERASE_ACTIVITY / GO / 33 / -0.52 / -1.43 / 0.032
CYTOSKELETON / GO / 345 / -0.27 / -1.42 / 0.010
PROTEIN_COMPLEX_BINDING / GO / 53 / -0.46 / -1.41 / 0.041
ALANINE_AND_ASPARTATE_METABOLISM / Genmapp / 21 / -0.44 / -1.40 / 0.091
RESPONSE_TO_DRUG / GO / 21 / -0.43 / -1.40 / 0.083
INTERMEDIATE_FILAMENT_CYTOSKELETON / GO / 21 / -0.58 / -1.40 / 0.067
INTERMEDIATE_FILAMENT / GO / 21 / -0.58 / -1.40 / 0.067
ANION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY / GO / 55 / -0.54 / -1.39 / 0.040
CYTOSKELETAL_PART / GO / 222 / -0.26 / -1.38 / 0.076

*ES, Enrichment Score, §NES, Normalized Enrichment Score

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