Table 2.
Top ten most sensitive gene set collections by median BMD for each chemical and cell type tested.
| Chemical Name | Most Sensitive Gene Sets (Pathways) | Probe IDs | Median BMD (MSigDB_C2), ppm | Median BMDL (MSigDB_C2), ppm |
|---|---|---|---|---|
| Acrolein (BEAS-2B cells) | REACTOME_REGULATION_OF_CHOLESTEROL_BIOSYNTHESIS_BY_SREBP_SREBF | SQLE_6736;INSIG2_21088;CYP51A1_92320 | 0.585727 | 0.39902 |
| NAKAMURA_ADIPOGENESIS_EARLY_DN | SERPINE2_27841,SERPINE2_27842;PDE6D_13043;LOX_21772 | 0.746618 | 0.4431965 | |
| NAKAMURA_ADIPOGENESIS_LATE_DN | SERPINE2_27841,SERPINE2_27842;PDE6D_13043;LOX_21772 | 0.746618 | 0.4431965 | |
| BIOCARTA_VDR_PATHWAY | SMARCC2_12862;BAZ1B_17476;ARID1A_26387 | 0.746681 | 0.3875 | |
| REACTOME_RUNX1_INTERACTS_WITH_CO_FACTORS_WHOSE_PRECISE_EFFECT_ON_RUNX1_TARGETS_IS_NOT_KNOWN | SMARCC2_12862;RUNX1_27815,RUNX1_6060;ARID1A_26387 | 0.746681 | 0.3875 | |
| LIU_COMMON_CANCER_GENES | NDUFS8_4528;LIMD1_17670;ATP6V0A1_11775 | 0.752497 | 0.464197 | |
| ZHAN_MULTIPLE_MYELOMA_MS_DN | OAS3_87750;MRPS31_92464;LETMD1_12057;DHPS_91625 | 0.760868 | 0.3744815 | |
| REACTOME_GAMMA_CARBOXYLATION_HYPUSINE_FORMATION_AND_ARYLSULFATASE_ACTIVATION | FN3K_92980;DPH2_91691;DHPS_91625;ARSJ_16411 | 0.7900935 | 0.343939 | |
| POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP | UGCG_11621;PLEC_14082;LRP8_13959;FLT3LG_25439 | 0.828844 | 0.397706 | |
| WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_36HR | EXOC6_19851;DYNLRB1_15749;CHUK_1342 | 0.834914 | 0.360823 | |
| 1-Bromopropane (BEAS-2B cells) | GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP | MAFF_27478,MAFF_28315;FTH1_92999,FTH1_93000;CD83_25945 | 2.24587 | 1.8379 |
| LEE_TARGETS_OF_PTCH1_AND_SUFU_UP | RND3_24211;MAGOHB_22392;IER5_15403 | 2.25517 | 1.88619 | |
| SCHEIDEREIT_IKK_TARGETS | NFKBIA_4568;NFKB1_4566;CYLD_17180 | 2.26819 | 1.85512 | |
| EPPERT_LSC_R | TGIF2_27952;PPP1R10_16865;NAB1_13978 | 2.40606 | 1.98632 | |
| LEE_CALORIE_RESTRICTION_NEOCORTEX_UP | RELB_28340;NFKBIA_4568;MAFF_27478,MAFF_28315;EIF2AK3_24919;CNOT2_17056 | 2.45342 | 2.0422 | |
| BIOCARTA_DEATH_PATHWAY | NFKBIA_4568;NFKB1_4566;BIRC3_11879 | 2.4806 | 2.06161 | |
| IKEDA_MIR133_TARGETS_UP | NFAT5_16375,NFAT5_27581;MAFK_26036;CYLD_17180 | 2.48805 | 2.05714 | |
| ZHAN_MULTIPLE_MYELOMA_PR_DN | JMJD1C_11504;FGF2_2405;CYLD_17180;ARID5B_88738,ARID5B_89998 | 2.50382 | 1.89154 | |
| KANG_CISPLATIN_RESISTANCE_UP | TENT5A_15343;MAFF_27478,MAFF_28315;IER5_15403;FTH1_92999,FTH1_93000 | 2.5370175 | 1.7680525 | |
| PID_HIV_NEF_PATHWAY | TRAF1_15516;NFKBIA_4568;NFKB1_4566;BIRC3_11879 | 2.579205 | 2.144825 | |
| 1,3-Butadiene (BEAS-2B cells) | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN | TM4SF1_12122;KDM6B_16198;HMOX1_3041 | 13.9794 | 7.78439 |
| ABBUD_LIF_SIGNALING_1_UP | SOCS3_15641;RGS4_20411;CEBPB_10745 | 21.3365 | 16.7624 | |
| CONRAD_STEM_CELL | KLF5_20609;KLF4_23258;CXCL5_15735 | 26.4384 | 21.1357 | |
| GROSS_HYPOXIA_VIA_ELK3_ONLY_UP | PPP1R15A_14098;CEBPB_10745;ADM_12873,ADM_140 | 28.2428 | 20.7323 | |
| LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP | HMOX1_3041;CXCL8_14324;CEBPB_10745;BMP2_22143;ADM_12873,ADM_140 | 28.2428 | 20.7323 | |
| SEMENZA_HIF1_TARGETS | HMOX1_3041;EDN1_2029;ADM_12873,ADM_140 | 28.2428 | 20.7323 | |
| ZAMORA_NOS2_TARGETS_UP | IER2_3213;HMOX1_3041;ADM_12873,ADM_140 | 28.2428 | 20.7323 | |
| SWEET_KRAS_TARGETS_DN | IRS2_21012;FOSL1_2463;DUSP4_1990;CXCL5_15735 | 28.5691 | 21.73905 | |
| HINATA_NFKB_TARGETS_KERATINOCYTE_DN | RUNX1_20078;GPRC5A_15162;DUSP4_1990 | 29.0199 | 22.4869 | |
| AMIT_SERUM_RESPONSE_240_MCF10A | TM4SF1_12122;PHLDA2_5123;ADRB2_151 | 29.6407 | 23.7457 | |
| Carbon Tetrachloride (BEAS-2B cells) | ANDERSEN_CHOLANGIOCARCINOMA_CLASS1 | TMEM156_25729;RGS4_20411;PTHLH_15144,PTHLH_5582;DCDC2_14713;CXCL6_15723 | 9.56328 | 7.98027 |
| CAFFAREL_RESPONSE_TO_THC_UP | ZFP36L1_14656;VEGFA_12596;MYC_4394;HIST1H2AC_93104;CPEB4_18785 | 11.2356 | 9.30456 | |
| MANN_RESPONSE_TO_AMIFOSTINE_UP | ZFP36L1_14656;MYC_4394;GDF15_18329 | 11.2356 | 9.30456 | |
| CHIN_BREAST_CANCER_COPY_NUMBER_UP | TGFB2_25683;PTGS2_5577;MYC_4394 | 11.6191 | 9.6667 | |
| DANG_MYC_TARGETS_DN | ZFP36L1_14656;PDGFB_5026;MYC_4394;CDKN2B_14415 | 12.3503 | 10.23368 | |
| GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN | TGFB2_25683;PLAUR_23941,PLAUR_5179;NR3C1_4689 | 13.0934 | 10.60316 | |
| WALLACE_PROSTATE_CANCER_UP | SOX4_6686;MYC_4394;GDF15_18329 | 13.347 | 9.58186 | |
| ZAMORA_NOS2_TARGETS_DN | ZFP36L1_14656;SOX4_6686;SOX17_89363;NFIA_18923;HSPB8_15039 | 13.347 | 11.0524 | |
| PID_LKB1_PATHWAY | TSC1_19318;SIK1_17023;MYC_4394 | 13.3507 | 9.14916 | |
| SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN | MYC_4394;ID1_14943;EREG_21427 | 13.3895 | 10.833 | |
| Trichloroethylene (BEAS-2B cells) | ROVERSI_GLIOMA_LOH_REGIONS | PPFIBP1_22884;NPFFR2_90111;GPRC5A_15162;DDHD1_10888 | 44.8416 | 29.00405 |
| HEIDENBLAD_AMPLIFIED_IN_PANCREATIC_CANCER | PPFIBP1_22884;MAL2_23815;CCN3_87436 | 47.0682 | 35.7006 | |
| OLSSON_E2F3_TARGETS_DN | NFKBIA_4568;MAL2_23815;HIST1H1C_2950 | 65.4966 | 47.7346 | |
| VANASSE_BCL2_TARGETS_UP | RELN_21362;MACC1_23235;HIST1H1C_2950 | 65.4966 | 41.4074 | |
| REACTOME_HDACS_DEACETYLATE_HISTONES | HIST2H4B_16248;HIST2H4A_33956;HIST2H2BF_93215;HIST1H2BJ_92661;HIST1H2AG_93175;HIST1H2AC_93104 | 67.48565 | 54.3204 | |
| SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER | HIST1H1C_2950;GDF15_2621;DHRS2_1857 | 69.8154 | 60.8512 | |
| RADMACHER_AML_PROGNOSIS | MAL_21284;FHL2_2423;EZR_25288;DAPK1_1752 | 72.244 | 51.08815 | |
| SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP | TENT5A_15343;OASL_89164;GPRC5A_15162;CCN3_87436 | 72.4401 | 49.10325 | |
| BASSO_HAIRY_CELL_LEUKEMIA_UP | SUSD5_15755;MAF_13534;IGFBP3_3270;DAPK1_1752 | 72.6945 | 46.20455 | |
| AIYAR_COBRA1_TARGETS_DN | ZNF532_20212;SOX4_6686;CLDN4_89537 | 73.9443 | 51.0529 | |
| Dichloromethane (BEAS-2B cells) | REACTOME_DEPURINATION | HIST2H4A_33956;HIST1H2BJ_92661;HIST1H2AC_93104 | 142.127 | 118.71 |
| FIGUEROA_AML_METHYLATION_CLUSTER_3_DN | PPP1R15A_14098;HIST1H2BJ_92661;HIST1H2AG_93175 | 158.016 | 130.242 | |
| COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN | SQSTM1_6740;CHI3L1_14316;BHLHE40_689 | 160.996 | 132.484 | |
| BOYLAN_MULTIPLE_MYELOMA_C_DN | KLF6_3626;JUN_89022;IRS2_21012 | 168.708 | 137.335 | |
| ZHAN_V2_LATE_DIFFERENTIATION_GENES | NR3C1_4689;KLF6_3626;IRF1_21247 | 168.708 | 137.335 | |
| BREUHAHN_GROWTH_FACTOR_SIGNALING_IN_LIVER_CANCER | SMAD7_12470;IRS2_21012;HBEGF_15347,HBEGF_2892 | 191.462 | 159.963 | |
| REACTOME_EGFR_DOWNREGULATION | SPRY1_18786;SH3KBP1_6296;HBEGF_15347,HBEGF_2892 | 191.462 | 159.963 | |
| REACTOME_SIGNALING_BY_EGFR | SPRY1_18786;SH3KBP1_6296;HBEGF_15347,HBEGF_2892 | 191.462 | 159.963 | |
| PID_EPO_PATHWAY | SOCS3_15641;NFKB1_4566;IRS2_21012 | 198.521 | 154.356 | |
| REACTOME_SIGNALING_BY_NON_RECEPTOR_TYROSINE_KINASES | SOCS3_15641;NR3C1_4689;HBEGF_15347,HBEGF_2892 | 198.521 | 159.963 | |
| Trichloroethylene (pHBEC cells) | KRIEG_HYPOXIA_VIA_KDM3A | NRP2_27606;KDM3A_3541;EBP_2015 | 28.1584 | 15.5176 |
| KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION | PCSK5_27656;NRP2_27606;LRBA_90214;AP1G1_21853 | 30.0328 | 16.13885 | |
| PID_VEGFR1_PATHWAY | VEGFA_28053;NRP2_27606;CD2AP_13562 | 30.6881 | 16.3157 | |
| KEGG_N_GLYCAN_BIOSYNTHESIS | MAN2A1_21283;MAN1A2_89683;MAN1A1_12471;ALG14_15409 | 30.87085 | 16.32435 | |
| REACTOME_SPHINGOLIPID_DE_NOVO_BIOSYNTHESIS | SGMS2_22813;SGMS1_13935;KDSR_14120 | 31.3726 | 16.5192 | |
| LUCAS_HNF4A_TARGETS_UP | RBKS_5758;MAN1A1_12471;KIFAP3_22932;EBP_2015 | 32.1622 | 16.56735 | |
| YU_MYC_TARGETS_DN | KLF2_16192;BTG1_26906;ABCA1_22891 | 32.2274 | 16.4188 | |
| REACTOME_FOXO_MEDIATED_TRANSCRIPTION | SIRT1_21308;RBL2_5761;BTG1_26906;BCL2L11_26447 | 32.29735 | 16.61775 | |
| PID_FOXO_PATHWAY | SIRT1_21308;SGK1_22771;RBL2_5761;BCL2L11_26447 | 32.48035 | 16.893 | |
| PID_HIF2PATHWAY | VEGFA_28053;SLC2A1_14159;SIRT1_21308 | 32.5934 | 16.8167 | |
| Dichloromethane (pHBEC cells) | MATTIOLI_MULTIPLE_MYELOMA_WITH_14Q32_TRANSLOCATIONS | MAF_13534;KLF4_23258;IL6R_17769 | 266.73 | 204.336 |
| DELACROIX_RAR_TARGETS_UP | RESF1_15542;DUSP1_1978;BHLHE40_689 | 323.565 | 232.508 | |
| SWEET_KRAS_TARGETS_UP | TPM1_28000;GADD45B_2570,GADD45B_28755;CLDN4_89537;BHLHE40_689;PGLS_16643 | 325.962 | 232.508 | |
| MENSE_HYPOXIA_UP | PPP1R15A_14098;MAFF_27478,MAFF_28315;KLF4_23258;INSIG1_3385;ENO2_2153;BHLHE40_689 | 326.754 | 236.46375 | |
| BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN | TPM1_28000;IGF1R_3254;IER2_3213 | 329.401 | 236.301 | |
| NAKAMURA_ADIPOGENESIS_EARLY_DN | TPM1_28000;IER2_3213;GDF15_18329 | 329.401 | 236.301 | |
| NAKAMURA_ADIPOGENESIS_LATE_DN | TPM1_28000;IER2_3213;GDF15_18329 | 329.401 | 236.301 | |
| RASHI_RESPONSE_TO_IONIZING_RADIATION_1 | IER2_3213;FOS_2461;DUSP1_1978 | 329.401 | 236.301 | |
| VANHARANTA_UTERINE_FIBROID_DN | MAFF_27478,MAFF_28315;KLF4_23258;IER2_3213;GADD45B_2570,GADD45B_28755 | 329.672 | 238.36025 | |
| AMIT_DELAYED_EARLY_GENES | MAFF_27478,MAFF_28315;FOSL1_2463;BHLHE40_689 | 329.943 | 240.4195 |