Transcriptomic analysis of breast cancer patients sensitive and resistant to chemotherapy: Looking for overall survival and drug resistance biomarkers

Carlos Alfredo Barrón-Gallardo, Mariel Garcia-Chagollán, Andrés de Jesús Morán-Mendoza, Raúl Delgadillo-Cristerna, María Guadalupe Martínez-Silva, Adriana Aguilar-Lemarroy, Luis Felipe Jave- Suárez

Supplementary table 2. KEGG pathway analysis of DEGs. Column 1 shows the KEGG pathway, in column 2 the DEGs are listed, and the column 3 groups the genes according its over or subexpression.

KEGG PATHWAY GENES EXPRESSION ACOT8, ACSL6, ADCY1, ALG3, AMD1, ASMT, ATP5MC1, ATP6V0A4, BAAT, CBS, CD38, CEL, CERS1, CHPT1, CKB, COQ3, DGKG, DOT1L, DPM1, EHMT2, ETNPPL, EXTL1, EZH1, EZH2, FADS1, G6PC2, GCNT2, GLDC, Over GLS2, GMPR, HPRT1, ISYNA1, ITPKA, NAPRT, NAT8L, NDUFS3, NSD2, OGDHL, PDE3B, PDE6C, PGS1, PIGP, PLA2G2D, PLA2G6, PLCG2, PPAT, SCD5, SMS, SMYD1, SYNJ2, UCK1, UGT2B15, UGT8, UMPS ACAD8, ACADM, ACER1, ACSL3, ACSS3, ADH1C, Metabolic pathways AKR1B10, ALDH1A1, ALOX15B, AOC3, ASAH1, B3GAT1, BPGM, CERS3, CHPF, CHST9, CHSY3, COX4I2, COX7A1, CYP26A1, CYP2J2, CYP4F8, DEGS2, DHCR24, DLD, DPYS, ENPP3, ETHE1, EXTL3, FUT2, FUT3, FUT6, GAD1, GALNT1, GALNT15, GALNT5, GNE, GSTA4, Sub GSTM3, GSTT2B, GUSB, H6PD, HAL, HMGCS2, HNMT, HSD17B2, HYAL3, HYI, IDH1, INPP5A, LDHC, MSMO1, NAMPT, NDUFA10, NEU1, NEU4, NNMT, P4HA3, PDE1A, PIP4K2B, PLA2G4E, PLA2G5, PLPP1, RDH12, ST6GAL2, ST6GALNAC1, TYRP1, UGT1A6, UGT1A7, UGT2B7, XDH ADCY1, BIRC5, CDK4, CKS2, CRKL, E2F2, FADD, FZD9, GNG3, IL12RB2, MYC, PLCG2, PMAIP1, RET, RXRB, Over SLC2A1, TERT, TRAF2 Pathways in cancer AGTR1, AR, ARHGEF12, COL4A1, CXCL8, EDNRA, FGF16, FGF5, FGF7, FN1, FZD1, GNG11, GNG12, GSTA4, GSTM3, GSTT2B, HEYL, IGF2, LAMA4, LAMB1, Sub LPAR1, MET, MITF, MMP2, PDGFA, PDGFRA, PDGFRB, RARA, RUNX1T1, TGFB2, TGFB3, VEGFC, ZBTB16 ACVR1C, AMH, CCL3L3, GDF15, IL12RB2, IL17D, IL17RA, IL17RB, IL1B, IL21, IL24, LTA, TNFRSF11B, Over Cytokine-cytokine TNFSF13B, TNFSF18 receptor ACKR3, ACVR1, ACVR2A, BMPR2, CCL27, CNTFR, interaction CTF1, CXCL14, CXCL17, CXCL8, IL13RA2, IL1R1, Sub IL20RB, IL22RA1, IL36RN, IL37, INHBA, INHBB, OSMR, TGFB2, TGFB3, TNFSF10 CALCB, CHRNA4, GABBR2, GABRP, GALR3, GCGR, GPR83, HTR1D, NPB, OPRD1, P2RX2, P2RX6, P2RY11, Over Neuroactive ligand TRH, VIPR2 receptor AGTR1, APLNR, AVPR1A, CALCRL, EDNRA, F2RL1, interaction GABRB3, GRIA4, GRIN2C, GRIN2D, HRH1, HTR2B, Sub LPAR1, NPFFR2, NPY1R, P2RY1, PTH1R, SLURP1, SSTR1 AREG, CDK4, EIF4EBP1, G6PC2, GNG3, MYC, PKN1, Over PPP2R3B, STK11, TCL1B PI3K-Akt signaling COL1A1, COL1A2, COL4A1, COL6A1, COL6A2, pathway COL6A3, COMP, FGF16, FGF5, FGF7, FN1, GNG11, GNG12, IGF2, ITGA5, ITGA9, KDR, LAMA4, LAMB1, Sub LPAR1, MET, OSMR, PDGFA, PDGFC, PDGFD, PDGFRA, PDGFRB, TEK, THBS2, TNXB, VEGFC, VWF AREG, CACNA1H, CACNB2, CRKL, DUSP2, DUSP9, IL1B, MAP3K4, MAPKAPK5, MAPT, MYC, NFATC3, Over TRAF2 MAPK signaling pathway CACNA1G, FGF16, FGF5, FGF7, GNG12, HSPA1A, HSPA2, IGF2, IL1R1, KDR, MET, PDGFA, PDGFC, Sub PDGFD, PDGFRA, PDGFRB, PLA2G4E, RASGRF2, TEK, TGFB2, TGFB3, VEGFC ADCY1, CACNA1H, CD38, ITPKA, ORAI1, P2RX2, Over P2RX6, PLCG2, PPIF, TNNC2, VDAC2 Calcium signaling pathway AGTR1, AVPR1A, CACNA1G, EDNRA, GRIN2C, GRIN2D, HRH1, HTR2B, PDE1A, PDGFA, PDGFC, PDGFD, Sub PDGFRA, PDGFRB, PLN ATF1, CDK9, CEBPE, DOT1L, EWSR1, MLF1, MLLT3, Over Transcriptional MYC, NSD2, RXRB, TLX1 misregulation in BCL6, CXCL8, ERG, ETV1, MET, MITF, PDGFA, RARA, cancer Sub RUNX1T1, RUNX2, ZBTB16 CDC25A, CRKL, E2F2, EZH2, EZR, GLS2, MYC, PLCG2, Over TRIM71 MicroRNAs in cancer BMPR2, ITGA5, MET, PDGFA, PDGFRA, PDGFRB, RECK, Sub SERPINB5, TGFB2, TIMP3, TNXB, TP63, TPM1 ADCY1, BUB3, CDK4, E2F2, ESPL1, HLA-C, HLA-DOA, Human T-cell HLA-DQB1, LTA, MYC, NFATC3, RAN, RANBP1, Over leukemia virus 1 RANBP3, SLC2A1, TBP, TERT, VDAC2 infection HLA-A, HLA-DRA, IL1R1, NRP1, TGFB2 Sub ACVR1C, AMH, BAMBI , E2F2, MYC, RBL1, TGIF2 Over TGF-beta signaling pathway ACVR1, ACVR2A, BMPR2, DCN, FBN1, FMOD, GREM1, Sub INHBA, INHBB, LTBP1, PITX2, TGFB2, TGFB3 EZR, FZD9, MYC, PLCG2 Over Proteoglycans in ARHGEF12, CAV1, CAV2, COL1A1, COL1A2, DCN, FN1, cancer FZD1, IGF2, ITGA5, KDR, LUM, MET, MMP2, TGFB2, Sub TIMP3

AFDN, BRAP, EXOC2, GNG3, PLA2G2D, PLA2G6, PLCG2 Over Ras signaling FGF16, FGF5, FGF7, GNG11, GNG12, IGF2, KDR, MET, pathway PDGFA, PDGFC, PDGFD, PDGFRA, PDGFRB, PLA2G4E, Sub PLA2G5, RASGRF2, TEK, VEGFC ATP6V0A4, CDK4, EIF4EBP1, FADD, FZD9, HLA-C, Over NFX1, PPP2R3B, RBL1, SCRIB, TBP, TERT Human papillomavirus COL1A1, COL1A2, COL4A1, COL6A1, COL6A2, COL6A3, COMP, FN1, FZD1, HEYL, HLA-A, ITGA5, infection Sub ITGA9, LAMA4, LAMB1, PATJ, PDGFRB, THBS2, TNXB, VWF

ADCY1, CCL3L3, CDK4, CGAS, CRKL, E2F2, EIF4EBP1, Human Over FADD, GNG3, HLA-C, IL1B, MYC, NFATC3, TRAF2 cytomegalovirus infection ARHGEF12, CXCL8, GNG11, GNG12, HLA-A, IL1R1, Sub PDGFRA BUB3, CDC14A, CDC25A, CDC45, CDK4, CDKN2D, E2F2, ESPL1, MCM2, MCM5, MYC, ORC6, PCNA, Over Cell cycle RAD21, RBL1, TTK TGFB2, TGFB3 Sub ADCY1, AFDN, AMH, GABBR2, HCN2, HTR1D, ORAI1, Over cAMP signaling PDE3B, VIPR2 pathway ATP1A1, ATP1B2, EDNRA, FXYD1, GRIA4, GRIN2C, Sub GRIN2D, MYL9, NPY1R, PLN, SSTR1 IL12RB2, IL17D, IL21, IL24, MYC Over JAK-STAT signaling CNTFR, CTF1, IL13RA2, IL20RB, IL22RA1, OSMR, pathway Sub PDGFA, PDGFRA, PDGFRB