Table 1a. Molecular signatures unique to the panobinostat and 5-AZA combination in JJN3 cells (Figure 4e).
| Gene set | No. of genes | Direction | Two-sided P-value | FDR |
|---|---|---|---|---|
| JISON_SICKLE_CELL_DISEASE_DN | 151 | Down | 0.006 | 0.491 |
| CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN | 16 | Up | 0.003 | 0.491 |
| SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_2 | 30 | Up | 0.003 | 0.491 |
| MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED | 36 | Up | 0.012 | 0.491 |
| KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP | 90 | Up | 0.016 | 0.491 |
| MCGARVEY_SILENCED_BY_METHYLATION_IN_COLON_CANCER | 25 | Up | 0.017 | 0.491 |
| BIOCARTA_UCALPAIN_PATHWAY | 16 | Up | 0.017 | 0.491 |
| NUMATA_CSF3_SIGNALING_VIA_STAT3 | 17 | Down | 0.019 | 0.491 |
| KIM_WT1_TARGETS_12 HR_DN | 177 | Down | 0.019 | 0.491 |
| KUNINGER_IGF1_VS_PDGFB_TARGETS_UP | 47 | Up | 0.020 | 0.491 |
| LABBE_TGFB1_TARGETS_UP | 80 | Up | 0.020 | 0.491 |
| SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER | 32 | Up | 0.021 | 0.491 |
| APPEL_IMATINIB_RESPONSE | 26 | Up | 0.021 | 0.491 |
| LEE_LIVER_CANCER_CIPROFIBRATE_UP | 37 | Up | 0.023 | 0.491 |
| PID_ECADHERIN_KERATINOCYTE_PATHWAY | 18 | Up | 0.025 | 0.491 |
| REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS | 19 | Up | 0.026 | 0.491 |
| KEGG_N_GLYCAN_BIOSYNTHESIS | 44 | Down | 0.027 | 0.491 |
| KUNINGER_IGF1_VS_PDGFB_TARGETS_DN | 35 | Up | 0.027 | 0.491 |
| ZHAN_MULTIPLE_MYELOMA_CD2_DN | 45 | Down | 0.027 | 0.491 |
| AIGNER_ZEB1_TARGETS | 23 | Up | 0.028 | 0.491 |
| REACTOME_CELL_JUNCTION_ORGANIZATION | 54 | Up | 0.028 | 0.491 |
| KEGG_TIGHT_JUNCTION | 107 | Up | 0.029 | 0.491 |
| VERRECCHIA_RESPONSE_TO_TGFB1_C2 | 24 | Up | 0.029 | 0.491 |
| REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING | 29 | Up | 0.029 | 0.491 |
| HELLER_SILENCED_BY_METHYLATION_UP | 224 | Up | 0.029 | 0.491 |
| BIOCARTA_FAS_PATHWAY | 29 | Down | 0.030 | 0.491 |
| REACTOME_G1_PHASE | 35 | Down | 0.030 | 0.491 |
| MEISSNER_BRAIN_HCP_WITH_H3K4ME2_AND_H3K27ME3 | 40 | Up | 0.030 | 0.491 |
| PID_HIVNEFPATHWAY | 32 | Down | 0.031 | 0.491 |
| REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE | 25 | Up | 0.032 | 0.491 |
| SHIN_B_CELL_LYMPHOMA_CLUSTER_2 | 27 | Down | 0.032 | 0.491 |
| ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF | 34 | Up | 0.032 | 0.491 |
| JOHANSSON_GLIOMAGENESIS_BY_PDGFB_DN | 18 | Up | 0.033 | 0.491 |
| REACTOME_STRIATED_MUSCLE_CONTRACTION | 18 | Up | 0.034 | 0.491 |
| LIANG_SILENCED_BY_METHYLATION_2 | 35 | Up | 0.034 | 0.491 |
| BIOCARTA_ARF_PATHWAY | 17 | Down | 0.034 | 0.491 |
| BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_UP | 20 | Up | 0.034 | 0.491 |
| CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 | 389 | Up | 0.035 | 0.491 |
| REACTOME_CELL_CELL_COMMUNICATION | 87 | Up | 0.035 | 0.491 |
| REACTOME_AXON_GUIDANCE | 207 | Up | 0.035 | 0.491 |
| BRACHAT_RESPONSE_TO_METHOTREXATE_UP | 23 | Up | 0.035 | 0.491 |
| RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP | 19 | Down | 0.036 | 0.491 |
| MIPS_28S_RIBOSOMAL_SUBUNIT_MITOCHONDRIAL | 30 | Down | 0.036 | 0.491 |
| KEGG_FOCAL_ADHESION | 168 | Up | 0.036 | 0.491 |
| REACTOME_RECYCLING_PATHWAY_OF_L1 | 26 | Up | 0.037 | 0.491 |
| HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN | 112 | Down | 0.037 | 0.491 |
| MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN | 41 | Up | 0.038 | 0.491 |
| CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP | 16 | Up | 0.038 | 0.491 |
| MATZUK_SPERMATOZOA | 81 | Up | 0.038 | 0.491 |
| MARTENS_TRETINOIN_RESPONSE_UP | 377 | Up | 0.038 | 0.491 |
| MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP | 70 | Up | 0.039 | 0.491 |
| DORSEY_GAB2_TARGETS | 22 | Up | 0.039 | 0.491 |
| LIAN_LIPA_TARGETS_6M | 34 | Up | 0.039 | 0.491 |
| VANTVEER_BREAST_CANCER_BRCA1_UP | 32 | Down | 0.040 | 0.491 |
| MISSIAGLIA_REGULATED_BY_METHYLATION_UP | 102 | Up | 0.041 | 0.491 |
| MIPS_55S_RIBOSOME_MITOCHONDRIAL | 77 | Down | 0.041 | 0.491 |
| VALK_AML_CLUSTER_15 | 23 | Up | 0.042 | 0.491 |
| REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION | 20 | Down | 0.042 | 0.491 |
| CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_UP | 55 | Up | 0.042 | 0.491 |
| SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 | 286 | Up | 0.042 | 0.491 |
| BIOCARTA_AGR_PATHWAY | 27 | Up | 0.042 | 0.491 |
| CROONQUIST_STROMAL_STIMULATION_UP | 45 | Up | 0.043 | 0.491 |
| NIELSEN_SYNOVIAL_SARCOMA_UP | 15 | Up | 0.043 | 0.491 |
| HUANG_GATA2_TARGETS_DN | 62 | Down | 0.043 | 0.491 |
| KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION | 91 | Up | 0.044 | 0.491 |
| ONKEN_UVEAL_MELANOMA_UP | 731 | Down | 0.045 | 0.491 |
| PID_S1P_S1P1_PATHWAY | 19 | Up | 0.045 | 0.491 |
| YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 | 59 | Up | 0.045 | 0.491 |
| ZHANG_TLX_TARGETS_DN | 91 | Up | 0.046 | 0.491 |
| GU_PDEF_TARGETS_DN | 25 | Up | 0.046 | 0.491 |
| ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN | 64 | Down | 0.047 | 0.491 |
| VILIMAS_NOTCH1_TARGETS_UP | 39 | Up | 0.047 | 0.491 |
| BURTON_ADIPOGENESIS_7 | 41 | Up | 0.047 | 0.491 |
| PID_INTEGRIN_A9B1_PATHWAY | 17 | Up | 0.047 | 0.491 |
| REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL | 62 | Up | 0.048 | 0.491 |
| ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP | 162 | Up | 0.048 | 0.491 |
| BAELDE_DIABETIC_NEPHROPATHY_UP | 56 | Up | 0.048 | 0.491 |
| MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP | 18 | Down | 0.048 | 0.491 |
| BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP | 26 | Up | 0.049 | 0.491 |
| REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS | 16 | Up | 0.049 | 0.491 |
| POTTI_CYTOXAN_SENSITIVITY | 30 | Up | 0.049 | 0.491 |
| GOLUB_ALL_VS_AML_DN | 18 | Up | 0.049 | 0.491 |
| MIPS_39S_RIBOSOMAL_SUBUNIT_MITOCHONDRIAL | 47 | Down | 0.049 | 0.491 |
| KIM_MYC_AMPLIFICATION_TARGETS_UP | 169 | Down | 0.049 | 0.491 |
| LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT | 67 | Up | 0.049 | 0.491 |
| PID_THROMBIN_PAR1_PATHWAY | 37 | Up | 0.049 | 0.491 |
| CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN | 42 | Up | 0.049 | 0.491 |
CAMERA results for the gene sets from the MSigDB from panobinostat- and 5-AZA-treated JJN3 cells. Data include the size of each set, direction of gene set alterations, two-sided P-value and FDR