Table-S3: The gene sets used in our work for marking each typical biological processes Angiogenesis Antigen processing machinery CD8 T effector Cell cycle DNA damage repair DNA replication EMT (1) EMT2 EMT3 FGFR3-related genees Immune checkpoint Mismatch repair Nucleotide excision repair Pan-F-TBRS WNT target CDH5 B2M CD8A ABL1 ALKBH2 DNA2 CLDN3 AXL FOXF1 FGFR3 CD274 EXO1 CCNH ACTA2 EFNB3 SOX17 HLA-A CXCL10 ANAPC1 ALKBH3 FEN1 CLDN7 FAP GATA6 TP63 CTLA4 LIG1 CDK7 ACTG2 MYC SOX18 HLA-B CXCL9 ANAPC10 APEX1 LIG1 CLDN4 LOXL2 SOX9 WNT7B HAVCR2 MLH1 CETN2 ADAM12 TCF12 TEK HLA-C GZMA ANAPC11 APEX2 MCM2 CDH1 ROR2 TWIST1 LAG3 MLH3 CUL4A ADAM19 VEGFA TAP1 GZMB ANAPC13 APLF MCM3 VIM TAGLN ZEB1 PDCD1 MSH2 CUL4B CNN1 TAP2 IFNG ANAPC2 ATM MCM4 TWIST1 TWIST2 ZEB2 PDCD1LG2 MSH3 DDB1 COL4A1 PRF1 ANAPC4 ATR MCM5 ZEB1 WNT5A TIGIT MSH6 DDB2 CTGF TBX21 ANAPC5 ATRIP MCM6 ZEB2 PCNA ERCC1 CTPS1 ANAPC7 BLM MCM7 PMS2 ERCC2 FAM101B ATM BRCA1 PCNA POLD1 ERCC3 FSTL3 ATR BRCA2 POLA1 POLD2 ERCC4 HSPB1 BUB1 BRIP1 POLA2 POLD3 ERCC5 IGFBP3 BUB1B CCNH POLD1 POLD4 ERCC6 PXDC1 BUB3 CDK7 POLD2 RFC1 ERCC8 SEMA7A CCNA1 CETN2 POLD3 RFC2 GTF2H1 SH3PXD2A CCNA2 CHAF1A POLD4 RFC3 GTF2H2 TAGLN CCNB1 CHEK1 POLE RFC4 GTF2H3 TGFBI CCNB2 CHEK2 POLE2 RFC5 GTF2H4 TNS1 CCNB3 CLK2 POLE3 RPA1 GTF2H5 TPM1 CCND1 DCLRE1C POLE4 RPA2 LIG1 CCND2 DDB1 PRIM1 RPA3 MNAT1 CCND3 DDB2 PRIM2 RPA4 PCNA CCNE1 DUT RFC1 SSBP1 POLD1 CCNE2 ENDOV RFC2 POLD2 CCNH ERCC1 RFC3 POLD3 CDC14A ERCC2 RFC4 POLD4 CDC14B ERCC3 RFC5 POLE CDC16 ERCC4 RNASEH1 POLE2 CDC20 ERCC5 RNASEH2A POLE3 CDC23 ERCC6 RNASEH2B POLE4 CDC25A ERCC8 RNASEH2C RAD23A CDC25B FAN1 RPA1 RAD23B CDC25C FANCA RPA2 RBX1 CDC26 FANCB RPA3 RFC1 CDC27 FANCC RPA4 RFC2 CDC45 FANCD2 SSBP1 RFC3 CDC6 FANCE RFC4 CDC7 FANCF RFC5 CDK1 FANCG RPA1 CDK2 FANCL RPA2 CDK4 FANCM RPA3 CDK6 GTF2H1 RPA4 CDK7 GTF2H2 XPA CDKN1A GTF2H3 XPC CDKN1B GTF2H4 CDKN1C GTF2H5 CDKN2A H2AFX CDKN2B HLTF CDKN2C HUS1 CDKN2D LIG1 CHEK1 LIG3 CHEK2 LIG4 CREBBP MBD4 CUL1 MDC1 DBF4 MGMT E2F1 MLH1 E2F2 MLH3 E2F3 MMS19 E2F4 MNAT1 E2F5 MPG EP300 MSH2 ESPL1 MSH3 FZR1 MSH4 GADD45A MSH5 GADD45B MSH6 GADD45G MUTYH GSK3B NEIL1 HDAC1 NEIL2 HDAC2 NEIL3 MAD1L1 NHEJ1 MAD2L1 NTHL1 MAD2L2 NUDT1 MCM2 OGG1 MCM3 PALB2 MCM4 PARP1 MCM5 PARP2 MCM6 PARP3 MCM7 PCNA MDM2 PER1 MYC PMS1 ORC1 PMS2 ORC2 PNKP ORC3 POLB ORC4 POLD1 ORC5 POLE ORC6 POLG PCNA POLH PKMYT1 POLL PLK1 POLM PRKDC POLQ PTTG1 PRKDC PTTG2 RAD1 RAD21 RAD17 RB1 RAD18 RBL1 RAD23A RBL2 RAD23B RBX1 RAD51C SFN RAD9A SKP1 RECQL4 SKP2 RECQL5 SMAD2 RIF1 SMAD3 RNF168 SMAD4 RNF4 SMC1A RNF8 SMC1B RPA1 SMC3 RPA2 STAG1 RPA3 STAG2 RPA4 TFDP1 RRM2B TFDP2 SETMAR TGFB1 SHPRH TGFB2 SMUG1 TGFB3 TDP1 TP53 TDP2 TTK TOPBP1 WEE1 TP53 YWHAB TREX1 YWHAE UBE2A YWHAG UBE2B YWHAH UBE2N YWHAQ UBE2V2 YWHAZ UNG ZBTB17 UVSSA WRN XAB2 XPA XPC XRCC1 XRCC4 XRCC5 XRCC6