WERNER_FIBRO_DN LEI_MYB_REGULATED_GENES BRCA1_OVEREXP_DN SUBCLASSES_DIFF P21_P53_MIDDLE_DN

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1 Supplemental Table S1. Full List of Up-Regulated Conserved Biological Modules Between Zebrafish Liver Tumor with Human Liver, Lung, Gastric, and Prostate Tumors LvCMs (ZF liver cancer vs. human liver cancers [Chen et al. 6 and Neo et al. 7 ]) LgCMs (ZF liver cancer vs. human lung cancers [Bhattacharjee et al. 2 and Garber et al. 11 ]) GsCMs (ZF liver cancer vs. human gastric cancers [Lam et al. 4 and Chen et al. 8 ]) PrCMs (ZF liver cancer vs. human prostate cancers [Dhanasekaran et al. 9 and Welsh et al. 10 ]) LEI_MYB_REGULATED_ GENES MRNA_PROCESSING_ MOREAUX_TACI_HI_VS_ LOW_ WERNER_FIBRO_ LEI_MYB_REGULATED_GENES BRCA1_OVEREXP_ MRNA_PROCESSING_ MRNA_PROCESSING_ CANCER_NEOPLASTIC_ MOREAUX_TACI_HI_VS_LOW_ LE_MYELIN_UP HSA01030_GLYCAN_STRUCTURES_ BIOSYNTHESIS_1 LE_MYELIN_UP HSA04110 IRS1_KO_ADIP_UP _RAPAMYCIN_ SMITH_HTERT_UP KREBPATHWAY MYC_ONCOGENIC_SIGNATURE _GLUTAMINE_ HSA04110 HCC_SURVIVAL_GOOD_VS_POOR_ HSA04110 JISON_SICKLE_DIFF HIPPOCAMPUS_DEVELOPMENT_ PRENATAL BRCA1_OVEREXP_ PROSTATE_ P21_P53_MIDDLE_ HSA03020_RNA_POLYMERASE LAMB_CYCLIN_D3_GLOCUS P21_P53_MIDDLE_ PEART_HISTONE_ ZHAN_MM_CD138_PR_VS_REST LAMB_CYCLIN_D3_GLOCUS TSA_CD4_UP ZHAN_MULTIPLE_MYELOMA _SUBCLASSES_DIFF ZHAN_MM_CD138_PR_VS_ REST BLEO_MOUSE_LYMPH_LOW_ 24HRS_ BASSO_REGULATORY_HUBS G1PATHWAY SERUM_FIBROBLAST_CORE_UP IDX_TSA_UP_CLUSTER3 A_DAMAGE_SIGNALING ET743_SARCOMA_48HRS_ PEART_HISTONE_ ZHAN_MULTIPLE_MYELOMA_ A_REPLICATION_ HOFFMANN_BIVSBII_BI_TABLE2 SUBCLASSES_DIFF MATSUDA_VALPHAINKT_ BRCA1_OVEREXP_ A_REPLICATION_ DIFF UVB_NHEK3_ALL CANCER_NEOPLASTIC_ GENOTOXINS_ALL_4HRS_REG GENOTOXINS_24HRS_DISCR KEGG BRCA1_OVEREXP_ UVB_NHEK3_C0 RCC_NL_UP CANCER_NEOPLASTIC_ HCC_SURVIVAL_GOOD_VS_ ADIP_DIFF_CLUSTER4 KEGG POOR_ HIPPOCAMPUS_ DEVELOPMENT_ PRENATAL HSA03020_RNA_ POLYMERASE HDACI_COLON_CUR_UP LEE_TS3_UP ET743_SARCOMA_72HRS_ FALT_BCLL_UP HESS_HOXAANMEIS1_ ET743_SARCOMA_ MRNA_PROCESSING GH_GHRHR_KO_24HRS RAPAMYCIN_ HDACI_COLON_CLUSTER6 RBPATHWAY BREASTCA_TWO_CLASSES HUMAN_CD34_ENRICHED _TRANSCRIPTION_FACTORS IDX_TSA_UP_CLUSTER3 UVB_NHEK3_C2 ADIP_DIFF_CLUSTER4 PEART_HISTONE_ CANCER_UNDIFFERENTIATED_ P21_P53_ANY_ (continued)

2 Supplemental Table S1. (Continued) LvCMs (ZF liver cancer vs. human liver cancers [Chen et al. 6 and Neo et al. 7 ]) LgCMs (ZF liver cancer vs. human lung cancers [Bhattacharjee et al. 2 and Garber et al. 11 ]) GsCMs (ZF liver cancer vs. human gastric cancers [Lam et al. 4 and Chen et al. 8 ]) HESS_HOXAANMEIS1_UP HDACI_COLON_CUR24HRS_UP G1_TO_S HSA03050_PROTEASOME ADIP_DIFF_CLUSTER5 HOFFMANN_BIVSBII_BI_ TABLE2 FLECHNER_KIEY_ TRANSPLANT_ WELL_UP BASSO_REGULATORY_ HUBS SERUM_FIBROBLAST_ CORE_UP FLECHNER_KIEY_ TRANSPLANT_ REJECTION_PBL_UP PROTEASOME_DEGRADATION CANCER_UNDIFFERENTIATED_ AMINOACYL_TRNA_BIOSYNTHESIS BRENTANI SERUM_FIBROBLAST_ SERUM_FIBROBLAST LEUCINE LEUCINE_ ET743_SARCOMA_48HRS_ TARTE_PLASMA_BLASTIC LIN_WNT_UP A_REPLICATION_ TRNA_SYNTHETASES _ GENOTOXINS_ALL_ CHANG_SERUM_RESPONSE_UP MANALO_HYPOXIA_ 4HRS_REG BRCA1_OVEREXP_ MENSSEN_MYC_UP CANCER_NEOPLASTIC_ O6BG_RESIST_ MEDULLOBLASTOMA KEGG _ LEE_TS3_UP MANALO_HYPOXIA_ VHL_NORMAL_UP HSA00970_AMINOACYL_TRNA_ BIOSYNTHESIS MRNA_PROCESSING _GLUTAMINE_ PROTEASOMEPATHWAY HDACI_COLON_CUR48HRS_UP HDACI_COLON_CLUSTER6 SHIPP_FL_VS_DLBCL_ RCC_NL_UP _GLUCOSE_ RNA_TRANSCRIPTION_ HUMAN_CD34_ENRICHED_ TRANSCRIPTION_ FACTORS ADIP_DIFF_CLUSTER4 P21_P53_ANY_ ET743_SARCOMA_ 72HRS_ BLEO_MOUSE_LYMPH_ HIGH_ 24HRS_ PrCMs (ZF liver cancer vs. human prostate cancers [Dhanasekaran et al. 9 and Welsh et al. 10 ])

3 ET743_SARCOMA_ G1_TO_S G2PATHWAY ADIP_DIFF_CLUSTER5 _RAPAMYCIN_ AS3_FIBRO_UP BREASTCA_TWO_CLASSES UVB_NHEK3_C2 CANCER_ UNDIFFERENTIATED_ BRENTANI MRNA_SPLICING HSA03050_PROTEASOME LIZUKA_G1_SM_G2 AS3_FIBRO_C3 PROTEASOME_ DEGRADATION INOS_ALL_UP SERUM_FIBROBLAST LEUCINE_ TARTE_PLASMA_BLASTIC CHANG_SERUM_RESPONSE_ UP MENSSEN_MYC_UP O6BG_RESIST_ MEDULLOBLASTOMA_ ZUCCHI_EPITHELIAL_UP _ MANALO_HYPOXIA_ HSA00970_AMINOACYL_ TRNA_ BIOSYNTHESIS MYC_TARGETS P53_SIGNALING ZELLER_MYC_UP _GLUTAMINE_ HDACI_COLON_CUR48HRS_ UP SHIPP_FL_VS_DLBCL_ LvCMs, liver conserved modules; LgCMs, lung conserved modules; GsCMs, gastric conserved modules; PrCMs, prostate conserved modules; ZF, zebrafish.

4 Supplemental Table S2. Full List of Down-Regulated Conserved Biological Modules Between Zebrafish Liver Tumor with Human Liver, Lung, Gastric, and Prostate Tumors LvCMs (ZF liver cancer vs. human liver cancers [Chen et al. 6 and Neo et al. 7 ]) LgCMs (ZF liver cancer vs. human lung cancers [Bhattacharjee et al. 2 and Garber et al. 11 ]) GsCMs (ZF liver cancer vs. human gastric cancers [Lam et al. 4 and Chen et al. 8 ]) PrCMs (ZF liver cancer vs. human prostate cancers [Dhanasekaran et al. 9 and Welsh et al. 10 ]) HSIAO_LIVER_SPECIFIC_GENES HSA00380_TRYPTOPHAN_ METABOLISM HCC_SURVIVAL_GOOD_VS_POOR_UP HSA04610_COMPLEMENT_AND_ COAGULATION_CASCADES AGEING_KIEY_SPECIFIC_ HSA04020_CALCIUM_SIGNALING_ PATHWAY BRCA_ER_POS TARTE_MATURE_PC HSA00071_FATTY_ACID_METABOLISM TARTE_MATURE_PC BRCA_PROGNOSIS_POS HSA04610_COMPLEMENT_AND_ ELECTRON_TRANSPORT_CHAIN COAGULATION_CASCADES HSA03320_PPAR_SIGNALING_PATHWAY FATTY_ACID_DEGRADATION LEE_DENA_ FATTY_ACID_METABOLISM FATTY_ACID_METABOLISM FLECHNER_KIEY_TRANSPLANT_ REJECTION_ BETA_ALANINE_METABOLISM HCC_SURVIVAL_GOOD_VS_POOR_UP FATTY_ACID_DEGRADATION HSA00071_FATTY_ACID_METABOLISM MITOCHONDRIAL_FATTY_ACID_ BETAOXIDATION HSA00260_GLYCINE_SERINE_AND_ THREONINE_METABOLISM LEE_MYC_ HSA00280_VALINE_LEUCINE_AND_ ISOLEUCINE_DEGRADATION VALINE_LEUCINE_AND_ISOLEUCINE_ HSA00640_PROPANOATE_METABOLISM DEGRADATION FETAL_LIVER_VS_ADULT_LIVER_GNF2 HSA00650_BUTANOATE_METABOLISM LEE_MYC_E2F1_ HSA00980_METABOLISM_OF_ XENOBIOTICS_BY_CYTOCHROME_ P450 EXTRINSICPATHWAY HSIAO_LIVER_SPECIFIC_GENES TYROSINE_METABOLISM HUMAN_MITODB_6_2002 HSA00120_BILE_ACID_BIOSYNTHESIS IDX_TSA_UP_CLUSTER6 PEPTIDE_GPCRS LEE_DENA_ HSA00640_PROPANOATE_METABOLISM MOOTHA_VOXPHOS HSA04080_NEUROACTIVE_LIGAND_ RECEPTOR_INTERACTION SANSOM_APC_4_ TARTE_MATURE_PC SANSOM_APC_5_ LEE_MYC_TGFA_ TYROSINE_METABOLISM BRCA_PROGNOSIS_POS VENTRICLES_UP ELECTRON_TRANSPORT HUMAN_TISSUE_LIVER LEE_E2F1_ HSA00350_TYROSINE_METABOLISM HSA00980_METABOLISM_OF_ XENOBIOTICS_ BY_CYTOCHROME_P450 SANSOM_APC_5_

5 Supplemental Table S3. Leading Edge Genes for Up-Regulated Biological Liver Conserved Modules to At Least Two Other Human Cancer Types BRCA1 OVEREXP CANCER NEOPLASTIC META UP CANCER UNDIFFERENTIATED META UP KEGG PEART HISTONE A REPLICATION ADIP DIFF CLUSTER4 HSP90B1 HDAC1 MELK MDM2 MDM2 ILF3 RPA1 ABCF1 HK1 HSPD1 PSMD2 HDAC1 HDAC1 TP53 PCNA IFRD2 PSMD1 MTHFD2 MTHFD2 TP53 TP53 RAD21 PRIM1 SNX5 PDCD11 LDHA RAD21 PCNA PCNA IFRD2 MCM7 MCM7 TRAP1 KDELR2 PCNA WEE1 WEE1 CTCF ORC5L HMGB2 CTPS PSMC4 GCLM E2F4 E2F4 CSE1L GMNN FEN1 PWP2H CCT4 SEC61B CCNB1 CCNB1 MCM7 MCM5 RRM2 SFRS11 CDC2 CCNB1 MCM7 MCM7 PPP2R1A MCM4 NAP1L4 EIF2B2 IARS CEBPG ORC5L ORC5L MCM5 RPA2 MCM5 TTIP2 RBM4 CDC2 CDC2 CDC2 RIOK3 MCM6 MCM4 ATIC MMP9 HMGB2 MCM5 ITM1 TFDP1 POLE2 SMC2 U2AF1 PSME2 DLG7 CDH1 MCM5 TFDP2 ORC1L MCM6 CCND1 ILF2 DPM1 MCM4 MCM4 RAN NMT1 NCBP2 MAD2L1 TFDP1 TFDP1 CCNB2 BYSL COL1A2 ILF2 MAD2L1 MAD2L1 MCM6 CCNB2 CCNB2 H2AFX MCM6 MCM6 EIF2S2 MRNA_ PROCESSING_ HSA04110 SERUM FIBROBLAST LEUCINE RAPAMYCIN GLUTAMINE MANALO HYPOXIA SF3B4 MDM2 MELK PSMD2 YARS CLIC1 ILF3 SFRS2 HDAC1 TUBB2C ACAT2 ARF1 ABCF1 DDX18 CPSF3 TP53 PCNA SF3B4 ACAT2 ACAT2 SFRS2 CPSF1 PCNA PRIM1 ILF3 RAB1A SF3B4 PSME3 RNPS1 WEE1 EFHC1 SFRS2 HSPA4 KARS ID1 CD2BP2 CCNB1 CDC2 LDHA MARS BZW1 PRC1 PTBP1 MCM7 FEN1 HSPA4 RAB14 DDX18 CTPS U2AF1 ORC5L RRM2 FDPS ETF1 BAZ1A RNU3IP2 SRPK1 CDC2 DLG7 PSMD1 PITPNB SFRS2 ATIC SNRPD1 FZR1 GMNN ETF1 CTPS LDHA CDC2 PRPF8 CCND1 HMMR EIF5 HSPA8 HSPA4 POLR3K SNRPB MCM5 TUBA1 PSMA5 PSMB5 DKC1 RRM2 LSM7 MCM4 KIFC1 HSPA8 ZNF259 IFRD2 SNRPD1 CUGBP2 TFDP1 MCM5 CSE1L HYOU1 AJB1 MCM5 CSTF3 MAD2L1 ANP32E SEC61B SYNCRIP PSMD1 NOL5A CPSF2 CCNB2 TYMS TOMM40 CSE1L SF1 MCM4 CUGBP1 MCM6 MCM4 CALR TOMM40 EIF5 MAD2L1 NCBP2 MAD2L1 CCNB1 KPNA3 CTPS MCM6 PBK UBE2N EIF2B2 HSPA8 DHFR ILF2 CCT4 PSMC2 SYNCRIP POLE2 WSB1 PTBP1 RNU3IP2 PWP2H BOP1 CCNB2 PSMD3 CCT4 DHCR7 DDX23 MCM6 NMT1 RTCD1 CSE1L CHAF1A H2AFX BYSL PTBP1 SEC61B SNRPD3 LMNB1 LDHB SNRPC TOMM40 WDR51A NUTF2 NMT1 CALR DHFR TUBA1 BYSL CCNB1 TIMM17A LDHB UBE2N ALG8 TIMM17A RNU3IP2 NOL5A NOL5A COPS3 MCM4 CHUK SFRS1 NCL DAP3 PSMD3 SCD SCD CCND1 PIK3R3 DDX19 SRPK1 ERH XBP1 NMT1 MRPL28 NPM3 BYSL NDUFA9 LDHB TUBA1 (continued)

6 Supplemental Table S3. (Continued) MRNA_ PROCESSING_ HSA04110 SERUM FIBROBLAST LEUCINE RAPAMYCIN GLUTAMINE MANALO HYPOXIA TIMM17A ALG3 ZMPSTE24 ALG8 NOL5A UBE2G2 MYST1 NCL SCD PIK3R3 DDX19 XBP1 RUVBL2 SC4MOL ERH MRPL28 SMARCC1 ILF2