1．1所需的依赖项

inferCNV使用R包猿，BiocGenerics，binhf，caTools，coda，硬币，dplyr，doparallel，刨边机，fastcluster，fitdistrplus，foreach，futile.logger，未来，gplots，ggplot2，HiddenMarkov，莱顿，phyclust，RANN，重塑，rjags，RColorBrewer，SingleCellExperiment，SummarizedExperiment，tidyr并从存档中导入函数GMD。

1．2安装

如果(!requireNamespace("BiocManager"， quiet = TRUE)) install.packages("BiocManager")::install("infercnv")

1.3可选的扩展

如果您想使用交互式热图可视化，请检查附加包RinferCNV_NGCHM安装包后宠物猫，tsvio而且NGCHMR。要安装可选软件包，在R命令窗口中输入以下命令:

install.packages("tibble") install.packages("devtools") devtools::install_github("bmbroom/tsvio") devtools::install_github("bmbroom/NGCHMR"， ref="stable") devtools::install_github("broadinstitute/inferCNV_NGCHM")

下载NGCHM java应用程序，在普通shell中输入以下命令:

wget http://tcga.ngchm.net/NGCHM/ShaidyMapGen.jar

2.1创建InferCNV对象

读入原始计数矩阵和元数据，填充infercnv对象

infercnv_obj = CreateInfercnvObject(raw_counts_matrix="../inst/extdata/ oligodendroglioma_annotations_downsampled.txt"， delim="\t"， gene_order_file="../inst/extdata/gencode_downsampled. example_only_dont_use .txt"， ref_group_names=c("小胶质细胞/巨噬细胞"，"少胶质细胞(非恶性)"))

## INFO[2022-11-02 16:49:10]解析矩阵:../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz ## INFO[2022-11-02 16:49:12]解析基因顺序文件:../inst/extdata/gencode_downsampled. example_only_dont_use .txt ## INFO[2022-11-02 16:49:12]解析单元注释文件:../inst/extdata/oligodendroglioma_annotations_downsampled.txt ## INFO [2022-11-02 16:49:12]::order_reduce:开始。## INFO [2022-11-02 16:49:12] .order_reduce(): expr和order match。## INFO [2022-11-02 16:49:12]::process_data:order_reduce: reduce from positional data, new dimensions (r,c) = 10338,184 Total=18322440.6799817 Min=0 Max=34215。## INFO [2022-11-02 16:49:12] num基因删除考虑提供的基因排序列表:399 = 3.8595473012188%删除。## INFO [2022-11-02 16:49:12] -filtering out cells < 100 or > Inf, remove 0 % of cells ## WARN[2022-11-02 16:49:12]如果您正在使用analysis_mode="subclusters"选项，请在运行infercnv之前使用"options(scipen = 100)"，否则您可能会在生成hclust时遇到错误。## INFO [2022-11-02 16:49:13] verifying infercnv_obj

2．2运行完整的默认分析

out_dir= tempfile() infercnv_obj_default = infercnv::run(infercnv_obj, cutoff=1， # cutoff=1适用于Smart-seq2, cutoff=0.1适用于10x Genomics out_dir=out_dir, cluster_by_groups=TRUE, plot_steps=FALSE，降噪=TRUE, HMM=FALSE, no_prelim_plot=TRUE, png_res=60)

##定心缩放数据矩阵

## pc_1 ##阳性:PSMD14, GCA, TANK, SCN2A, MARCH7, CSRNP3, TTC21B, SCN1A, SPC25, DHRS9 ## BBS5, FASTKD1, PPIG, AKIRIN1, NDUFS5, RRAGC, MACF1, UTP11L, PPIEL, PHOSPHO2 ## FHL3, PABPC4, SF3A3, PPIE, INPP5B, KLHL23, TRIT1, C1orf122, CAP1, MANEAL ##阴性:PPM1A, DHRS7, MNAT1, TRMT5, SLC38A6, HIF1A, SNAPC1, LINC00643, PCNXL4, DDHD1 FERMT2, WDR89, GNPNAT1, GMFB, PPP2R5E, CGRRF1, STYX, RTN1, SOCS4, PSMC6 MAPK1IP1L, FBXO34, ATG14, TXNDC16, JKAMP, KTN1, L3HYPDH, PELI2, C14orf166, KIAA0586 ## pc2 ##阳性:TMEM219, KCTD13, aspd1, TAOK2, SEZ6L2, HIRIP3, CDIPT, ALDOA, MVP, PAGR1 ## PPP4C, PRRT2, MAZ, YPEL3, KIF22, QPRT, MAPK3, SULT1A4, SLX1B, CORO1A ## BOLA2, BOLA2B, SPNS1, SLX1A, NFATC2IP, SULT1A3, TUFM, ADCK1, GALC, SNW1, SPATA7, SLIRP, ZC3H14, ALKBH1 ## TTC8, SPTLC2, FOXN3, AHSA1, EFCAB11, VIPAS39, tstz1, POMT2 ## CALM1, ZDHHC22, KIAA1737, RPS6KA5, TGFB3, SMEK1 ## pc_3 ##阳性:CAND1, TMBIM4, DYRK2, MDM1, NUP107, RAP1B, LLPH, SLC35E3, LEMD3, MDM2 ## CPM, GNS, CPSF6, LYZ, TBK1, YEATS4, XPOT, FRS2, C12orf66, SRGAP1 ## CCT2, TMEM5, PPM1H, MON2, RAB3IP, USP15, CTDSP2, CNOT2, SDF2, FAM222B, KIAA0100, ALDOC, PIGS, ARHGEF26, ARHGEF26- as1 ## RAP2B, P2RY1, RNPC3, DPH5, MBNL1, SLC30A7, SLC44A1, ABCA1, FSD1L, EXTL2 ## NIPSNAP3A, FKTN, RTCA, TMEM38B, HIAT1, P2RY12, SMC2, SLC35A3, ZNF462, KLF4 ## pc4 ##阳性:MRPL46, NTRK3, KLHL25, AKAP13, MRPS11, DET1, AEN, MFGE8, ABHD2, POLG ## PEX11A, AP3S2, IDH2, C15orf38-AP3S2, C15orf38, CIB1, NGRN, CRTC3, MAN2A2, unc45a# # HDDC3, VPS33B, CHD2, RGMA, IGF1R, LRRC28, MEF2A, LINS, ASB7, VIMP ##阴性:RBM12, NFS1, CPNE1, ROMO1, ERGIC3, CEP250, EIF6, RBM39, EDEM2, trpc4ap# # PHF20, GSS, SCAND1, ACSS2, LINC00657, GGT7, EPB41L1, TP53INP2, AAR2, NCOA6 ## DLGAP4, PIGU, C20orf24, NDRG3, MAP1LC3A, SOGA1, DYNLRB1, SAMHD1, ITCH, RBL1 ## pc5 #阳性:STX17, ERP44, NR4A3, INVS, SEC61B, TEX10, ALG2, MSANTD3, MSANTD3- tmeff1, TGFBR1 ## LPPR1, TBC1D2, MRPL50, TRIM14, ZNF189, NANS, ANP32B, TMEM246, C9orf156, RNF20 ## XPA, SMC2, NCBP1, NIPSNAP3A, TSTD2, ABCA1, TMOD1, SLC44A1, ZNF510, fsd1l# #阴性:ZNF160, ZNF415, ZNF83, ZNF331, MYADM, ZNF528, NDUFA3, ZNF880, ZNF610, ZNF480 ## TFPT, PRPF31, LENG1, MBOAT7, TSEN34, RPS9, LILRA4, LAIR1, TTYH1, LENG8 ## LILRB4, RDH13, HSPBP1, RPL28, SHISA7, ISOC2, ZNF580, ZNF581, ZNF542, ZNF583

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:RFC1, RPL9, KLHL5, LIAS, UGDH, TMEM156, UGDH- as1, TLR1, KLF3, SMIM14 ## PGM2, RELL1, UBE2K, ARAP2, TBC1D19, pds5, rbgl, APBB2, ANAPC4, DHX15 ## UCHL1, PACRGL, LCORL, DCAF16, LIMCH1, MED28, LAP3, CD151, PIDD, SLC25A22, CEND1, POLR2L, PDDC1, CHID1 ## TMEM80, TOLLIP, DEAF1, IRF7, MOB2, PHRF1, SNHG9, RPS2, IFITM10, TBL3 ## NDUFB10, NTHL1, MSRB1, FAHD1, NUBP2, HAGH, mrsb3, TSC2, CRAMP1L ## pc2 ##阳性:APC2, C19orf25, MBD3, UQCR11, SCAMP4, BTBD2, MOB3A, AP3D1, PLEKHJ1, RNPS1 ## ECI1, E4F1, ABCA3, TBC1D24, ATP6V0C, MLST8, TRAF7, AMDHD2, SF3A2, PKD1 ## TSC2, NTHL1, TBL3, SNHG9, CEMP1, RPS2, NDUFB10, TBL3, SNHG9, CEMP1, RPS2, NDUFB10, OAZ1, MSRB1, FAHD1 ##阴性:ZNF131, NIM1, NIPBL, SLC1A3, SEPP1, HMGCS1, SKP2, C5orf42, FBXO4, LMBRD2 ## C5orf28, C5orf51, NUP155, BRIX1, PAIP1, WDR70, RAD1, OXCT1, NNT, lifr# # AMACR, RPL37, MRPS30, DAB2, PRKAA1, SUB1, TTC33 ## pc3 ##阳性:PSMC5, TEX2, CCDC47, POLG2, FTSJ3, STRADA, DDX42, DDX5, TACO1, MIR3064 ## MIR5047, DCAF7, CEP95, TANC2, SMURF2, PLEKHM1P, METTL2A, LRRC37A3, MED13, AMZ2P1 ## INTS2, BCAS3, GNA13, PRKCA, PPM1D, CACNG4, APPBP2, HELZ, PRKCA, PLXNA1, SEC61A1, CHCHD6, ZXDC, RUVBL1, SLC41A3 ## CCDC14, KALRN, OSBPL11, UMPS, SNX4, ZNF148, EEFSEC, MYLK, PTPLB, RPN1 ## SEC22A, RAB7A, SEMA5B, ACAD9, HSPBAP1, ISY1, DTX3L, CNBP, PARP9, COPG1 ## PC_ 4 ##阳性:SYNJ2BP, MED6, COX16, SMOC1, SRSF5, PCNX, KIAA0247, ZFYVE1, RBM25, PSEN1 ## NUMB, ACOT2, PNMA1, ELMSAN1, PTGR2, CRY1, MTERFD3, ZNF410, C12orf23, ric8b# # POLR3B, FAM161B, TCP11L2, CKAP4, COQ6, C12orf75, ALDH6A1, APPL2, LIN52, ABCD4 ##阳性:MOSPD3, ACTL6B, GNB2, GIGYF1, TSC22D4, POP7, C7orf61, MEPCE, ZCWPW1, SLC12A9 ## PILRA, PILRB, TRIP6, SRRT, ACHE, AP1S1, PLOD3, ZNHIT1, RABL5 ## CUX1, PRKRIP1, ORAI2, ALKBH4, NDN, MKRN3, SNRPN, SNURF, HERC2P7, UBE3A ## pc5 ##阳性:FGFR1OP, RNASET2, RPS6KA2, MLLT4, MPC1, SFT2D1, THBS2, QKI, C6orf120, CAHM ## LINC00574, AGPAT4, DLL1, FAM120B, MAP3K4, PSMB1, TBP, LPAL2, PDCD2, MRPL18 ## TCP1, SRD5A1, MTRR, NSUN2, CCDC127, MED10, SDHA, FASTKD3, MRPL36, PDCD6 ## Negative: SEC61B, NR4A3, ALG2, STX17, TGFBR1, TBC1D2, ERP44, TRIM14, NANS, invs# # ANP32B, ECHDC1, RNF146, TEX10, kia0408, TRMT11, HINT3, NCOA7, C9orf156, mantd3 ## PTPRK, msntpff1, EPB41L2, XPA, LPPR1, AKAP7, MRPL50, ZNF189, TMEM246, NCBP1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:NTHL1, TBL3, SNHG9, RPS2, NDUFB10, MSRB1, FAHD1, HAGH, NUBP2, SPSB3 ## MRPS34, NME3, MAPK8IP3, CRAMP1L, TELO2, CLCN7, C16orf91, UNKL, GNPTG, BAIAP3 ## UBE2I, SOX8, LMF1, CHTF18, RPUSD1, NARFL, HAGHL, WSCD1, MIS12, C1QBP ##阴性:NFASC、MDM4、CNTN2、PIK3C2B、RBBP5、PPP1R15B、DSTYK、TMCC2、SNRPE、ZBED6 ## CDK18、ZC3H11A、NUCKS1、ATP2B4、RAB7L1、BTG2、SLC41A1、ADORA1、SRGAP2、TMEM183A ## GLMN、BTBD8、RPAP2、CDC7、ZNF644、RPL5、ZNF326、CYB5R1、LRRC8D、RUSC2、STOML2、PIGO、FANCG、VCP、DNAJB5 ## IL11RA、KIAA1161、FAM219A、GALT、NUDT2、RPP25L、DCTN3、SIGMAR1、UBAP1、ATP5H ## ARMC7、DCAF12、ICT1、NT5C、HN1、UBAP2、CDR2L、SUMO2、HID1、UBE2R2 ##CD27-AS1, TNFRSF1A, TAPBPL, VAMP1, NACA, MRPL51, PRIM1, SNORA48, PARP11, LRP1 ## TULP3, RHNO1, SHMT2, NRIP2, R3HDM2, ITFG2, FKBP4, ARHGAP9, DCP1B, MARS ## ADIPOR2, DDIT3, WNK1, KIF5A, PIP4K2C, NINJ2, DTX3 ## pc3 ##阳性:IFI27L2, KIAA0196, SQLE, NSMCE2, DICER1, MTSS1, DDX24, TRIB1, TATDN1, SNHG10, RNF139, UNC79, GLRX5, TRMT12, MYC, FAM91A1, UBR7 ## C14orf132, FAM49B, WDYHV1, ATG2B, ZHX1, ASAP1, C14orf142, C8orf76, GSKIP, EFR3A ##阴性:TSTD2, NCBP1, XPA, C9orf156, ANP32B, NANS, TRIM14, TBC1D2, TGFBR1, ALG2 ## SEC61B, NR4A3, STX17, ERP44, INVS, TEX10, MSANTD3, MSANTD3- tmeff1, LPPR1, MRPL50 ## COMMD1, CCT4, B3GNT2, FAM161A, EHBP1, WDPCP, TIA1, C2orf42, XPO1, ZNF189 ## PC_ 4 ##阳性:ACSS2, GSS, GGT7, TRPC4AP, TP53INP2, NCOA6, EDEM2, PIGU, EIF6, CEP250 ## MAP1LC3A, ERGIC3, CPNE1, DYNLRB1, RBM12, NFS1, ITCH, ROMO1, RBM39, PHF20 ## AHCY, VPS29, SCAND1, FAM216A, LINC00657, EIF2S2, GPN3, EPB41L1, AAR2, ARPC3 ##阴性:POLG, ABHD2, PEX11A, MFGE8, AEN, AP3S2, DET1, C15orf38-AP3S2, MRPS11, C15orf38 ## MAN2A2, UNC45A, CRTC3, IDH2, NGRN, MRPL46, HDDC3, CIB1, VPS33B, NTRK3 ## CHD2, RGMA, KLHL25, AKAP13, IGF1R, ZNF592, SEC11A, NMB, LRRC28, WDR73 ## pc5 ##阳性:SGTB, NLN, TRAPPC13, TRIM23, PPWD1, CWC27, RNF180, IPO11, DIMT1, KIF2A ## ZSWIM6, SMIM15, ADAMTS1, NDUFAF2, APP, N6AMT1, LTN1, GABPA, ATP5J, RWDD2B ## ERCC8, JAM2, USP16, PLK2, CCT8, MRPL39, BACH1, TIAM1, NCAM2, GPBP1 ##阴性:Mfng, cdc42ep1, gga1, pdxp, lgals1, h1f0, gcat, ankrd54, eif3l, polr2f# # pla2g6, maff, tmem184b, csnk1e, ddx17, cby1, tomm22, josd1, gtpbp1, sun2 ## dnal4, nptxr, pdgfb, rpl3, syngr1, tab1, atf4, rps19bp1, tnrc6b, adsl

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:BANP, KLHDC4, MAP1LC3B, IRF8, COX4I1, EMC8, CRISPLD2, USP10, COTL1, SUDS3 ## TAOK3, PEBP1, VSIG10, WSB2, TAF1C, RFC5, FBXO21, JRK, FBXW8, CASP2 ## GSTK1, FAM131B, MTRNR2L6, RNFT2, ZFYVE27, ARC, CRTAC1, AVPI1, ZYX, R3HCC1L ##阴性:SCFD2, FIP1L1, DANCR, SGCB, DCUN1D4, OCIAD1, CHIC2, FRYL, PDGFRA, NFXL1 ## SRD5A3, COMMD8, GNPDA2, TMEM165, GUF1, CLOCK, ATP8A1, EXOC1, AASDH, PPAT ## SLC30A9, PAICS, SRP72, NOA1, POLR2B, LPHN3, UBA6, CXCL16, RNF167, ARRB2, PELP1, MED11, PFN1, MYBBP1A ## XAF1, SPAG7, UBE2G1, C17orf100, TXNDC17, RNASEK, WSCD1, ANKFY1, CAMTA2, MIS12 ## C17orf49, ZFP3, DERL2, RPAIN, ZNF232, CYB5D2, ACADVL, C1QBP, ZNF594, NUP88 ## Negative:COG1, FAM104A, CD300A, SSTR2, C17orf80, BTBD17, SLC39A11, SOX9, CDC42EP4, SLC9A3R1 KCNJ16, TTYH2, RPL38, ABCA8, PRKAR1A, NAT9, AMZ2, LINC00674, KPNA2, TMEM104 ## C17orf58, BPTF, FDXR, NOL11, PSMD12, HID1, HELZ, SNX19, NTM, IGSF9B, JAM3, NCAPD3, VPS26B, THYN1 ## ACAD8, B3GAT1, SYNJ2BP, MED6, PCNX, ZFYVE1, RBM25, PSEN1, NUMB, ACOT2 ## PNMA1, EML1, CYP46A1, ELMSAN1, EVL, YY1, CCNK, PTGR2, FAM161B, COQ6 ##FAM21C, AGAP4, PARG, ZNF485, ALOX5, VSTM4, CXCL12, ZNF32, ZNF22, ZNF239 ## NCOA4, RASSF4, ARHGAP22, BMS1P1, HNRNPF, GLUD1P7, MAPK8, FAM21B, BMS1P2, BMS1P6 ## AGAP9, ZNF488, BMS1P5, CSGALNACT2, TIMM23, BMS1, ZNF33B, AGAP6, ZNF37BP, HSD17B7P2 ## PC_ 4 ##阳性:GEMIN2, TRAPPC6B, PNN, CTAGE5, SEC23A, KLHL28, LINC00639, FAM179B, TMX1, TRIM9 ## NIN, PYGL, PRPF39, MBIP, ATL1, MAP4K5, FKBP3, ATP5S, MDGA2, RPS29 ## MIS18BP1, BRMS1L, RPL36AL, L2HGDH, MGAT2, DNAAF2, ARF6, ar7orf55, MKRN1, UBN2, NDUFB2, ZC3HAV1, BRAF ## TRIM24, AHSA2, USP34, CREB3L2, C2orf74, XPO1, MRPS33, PEX13, FAM161A, DGKI ## REL, CCT4, AGK, TMED8, PTN, VIPAS39, AHSA1, COMMD1, GSTZ1, SPTLC2 ## PC_ 5 ##阳性:SYNJ2BP, MED6, PCNX, ZFYVE1, RBM25, PSEN1, NUMB, ACOT2, PNMA1, ELMSAN1 ## PTGR2, ZNF410, FAM161B, COQ6, ALDH6A1, LIN52, UBIAD1, MTOR, EXOSC10, srm# # TARDBP, DFFA, PGD, KIF1B, ABCD4, UBE4B, NMNAT1, CNTLN, PSIP1, SNAPC3 ## Negative: NUP88, RPAIN, RABEP1, ZNF594, C1QBP, ZNF232, DERL2, ZFP3, CAMTA2, MIS12 ## SPAG7, WSCD1, PFN1, TXNDC17, RNF167, SLC25A11, PLD2, C17orf100, PSMB6, CXCL16 ## XAF1, MED11, ARRB2, RNASEK, PELP1, MYBBP1A, UBE2G1, C17orf49, MARCH5, EXOC6

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:CHRNB1, NLGN2, ZBTB4, TMEM256, POLR2A, GPS2, EIF4A1, EIF5A, CTDNEP1, GABARAP ## PHF23, DVL2, ACADVL, C17orf49, RNASEK, XAF1, ZNF594, RABEP1, C17orf100, ZNF232 ## NUP88, TXNDC17, RPAIN, DERL2, ZFP3, MIS12, C1QBP, WSCD1, CAMTA2, AMZ1 ##阴性:MRPL42, UBE2N, CRADD, EEA1, CCDC41, ACTR6, SCYL2, BTG1, TMCC3, ANO4 ## ATP2B1, NDUFA12, ARL1, NR2C1, GNPTAB, POC1B, ccddc53, NUP37, DUSP6, ASCL1 ## NT5DC3, C12orf29, HSP90B1, RSU1, STAM, C12orf73, FAM188A, NSUN6, CCDC59, ARL5B ## pc2 ##阳性:PTPN1, ADNP, TMEM189, DPM1, UBE2V1, MOCS3, ATP9A, RNF114, ZFP64, BCAS1 ## SLC9A8, ZFAS1, ARFGEF2, PFDN4, CSE1L, ZNFX1, STAU1, DDX27, DOK5, CSTF1 ## RTFDC1, BMP7, RAE1, MTRNR2L3, STX16, NPEPL1, ZNF789, ZNF394 ##阴性:ING2, RWDD4, CDKN2AIP, AGA, TRAPPC11, SPCS3, STOX2, GPM6A, SH3D19, PET112 ## RPS3A, ARFIP1, TRIM2, FBXW7, KIAA0922, DCLK2, GLRA3, TLR2, PRMT10, ZKSCAN8 ## PLRG1, IRF2, TMEM184C, CTSO, SLC10A7, CEP44, LSM6, PDGFC, ZSCAN9, FBXO8 ## PC_ 3 ##阳性:ATP6V1H, RB1CC1, TCEA1, PCMTD1, LYPLA1, UBE2V2, MRPL15, TMEM68, TGS1, ERLIN2 ## PROSC, DUSP26, BRF2, RNF122, RPS20, EIF4EBP1, MAK16, ASH2L, TTI2, FUT10 ## LSM1, CHCHD7, PPP2CB, BAG4, IMPAD1, DDHD2, ZCCHC8, UBXN8, CLIP1, VPS33A ##阴性:TBK1, GNS, XPOT, LEMD3, C12orf66, LLPH, TMBIM4, CAND1, DYRK2, SRGAP1 ## MDM1, RAP1B, TMEM5, NUP107, NMI, RND3, RIF1, SLC35E3, PPM1H, MMADHC ## KIF5C, ARL5A, EPC2, CACNB4, STAM2, MDM2, MON2, PAPOLA, VRK1, GSKIP ## pc4 ##阳性:TRPC4AP, GSS, EDEM2, EIF6, ACSS2, CEP250, CPNE1, ERGIC3, GGT7, RBM12 ## NFS1, TP53INP2, ROMO1, NCOA6, RBM39, PIGU, PHF20, MAP1LC3A, DYNLRB1, SCAND1 ## ITCH, LINC00657, AHCY, EPB41L1, AAR2, EIF2S2, DLGAP4, RALY, C20orf24, PXMP4 ##阴性:GCC2、ST6GAL2、LIMS1、UXS1、RANBP2、NCK2、SEPT10、C2orf49、RGPD5、GPR45 ## LINC00116、MRPS9、MERTK、MAP4K4、RNF149、ZC3H8、RPL31、PDCL3、TTL、CHST10 ## AFF3、REV1、EIF5B、TXNDC9、MRPL30、MITD1、MGAT4A、LIPT1、NR1H3、COX15、DNMBP、HPS1、ERLIN1、CHUK、CWF19L1、BLOC1S2 ## SFXN2、WBP1L、SCD、ARL3、R3HCC1L、C10orf32、TRIM8、LINC00263、AS3MT、NT5C2 ## DCTPP1、LDB1、SEC31B、ACTR1A、PPRC1、NOLC1、GBF1、INA、FBXL15、TMEM180 ##阴性:Med28, dcaf16, lcorl, pacrgl, lap3, dhx15, anapc4, qdpr, rbpj, tbc1d19 ## tapt1-as1, arap2, rell1, fam200b, pgm2, fbx15, klf3, tlr1, cc2d2a, tmem156 ## rab28, klhl5, wdr1, rfc1, rpl9, acox3, lias, sh3tc1, ugdh, ugdh - as1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:MTX1, KRTCAP2, GBAP1, DPM3, GBA, SCAMP3, SLC50A1, CLK2, FDPS, EFNA1 ## RUSC1, ASH1L, ADAM15, YY1AP1, DAP3, MSTO1, GON4L, FLAD1, SYT11, CKS1B ## RIT1, KIAA0907, SHC1, ARHGEF2, SSR2, PYGO2, UBQLN4, PMVK, LAMTOR2, ADAR ##阴性:CELSR2, PSRC1, SARS, SORT1, TMEM167B, WDR47, CLCC1, GPSM2, STXBP3, prpf38b# PRMT6, AMY2B, RNPC3, DPH5, SLC30A7, EXTL2, RTCA, GSTM3, HIAT1, CAP1 ## PPT1, TRIT1, RLF, COL9A2, ZMPSTE24, PPIE, PABPC4, SMAP2, SLC35A3, CSF1 ## pc2 ##阳性:RAB4A, RHOU, NUP133, RNF187, TAF5L, GALNT2, COG2, TRIM11, AGT, C1orf198 ## GUK1, TTC13, MRPL55, ARV1, C1orf35, C1orf131, ARF1, SCAMP3, GBA, CLK2 ## FDPS, RUSC1, GBAP1, GNPAT, ASH1L, MTX1, jmaip2, EXOC8, MSTO1, CEP350, QSOX1, RASAL2, ACBD6 ## ASTN1, XPR1, RFWD2, TNR, STX6, RABGAP1L, GLUL ## RC3H1, ZBTB37, NPL, GAS5, DHX9, NMNAT2, DARS2, SMG7, KLHL20, ARPC5 ## pc3 ##阳性:SHC1, CKS1B, FLAD1, PYGO2, ADAM15, EFNA1, PMVK, SLC50A1, ADAR, DPM3 ## C1orf43, CHRNB2, HAX1, UBAP2L, KRTCAP2, GBA, SCAMP3, CLK2, MTX1, GBAP1 ## FDPS, RUSC1, ASH1L, MSTO1, YY1AP1, DAP3, GON4L, SYT11, RIT1, KIAA0907 ##阳性:IL10, EIF2D, SRGAP2, SLC41A1, CD55, RAB7L1, NUCKS1, CD46, CDK18, HSD11B1 ## TMCC2, DSTYK, SYT14, RBBP5, RCOR3, CNTN2, INTS7, NFASC, RPL21P28, TMEM206 ## MDM4, PIK3C2B, NENF, SNRPE, ZBED6, PPP1R15B, ATF3, ZC3H11A, NSL1, ANGEL2 ## pc_4 ##阳性:IFI44, TTLL7, DNAJB4, PRKACB, RPF1, CLCA4, GTF2B, SH3GLB1, ODF2L, PKN2 ## GNG5, DDAH1, SEP15, FUBP1, CCBL2, BCL10, C1orf52, LRRC8D, ZNF326, FAM73A ## USP33, ZNF644, CDC7, ZZZ3, AK5, BTBD8, PIGK, GLMN, PMF1, SLC25A44, LMNA, PAQR6, LAMTOR2, SMG5, UBQLN4, SSR2, C1orf85 ## CCT3, C1orf61, ARHGEF2, MEF2D, APOA1BP, KIAA0907, GPATCH4, RIT1, BCAN, SYT11 ## ISG20L2, GON4L, RRNAD1, DAP3, MRPL24, YY1AP1, HDGF, MSTO1, PRCC, ASH1L ## pc5 ##阳性:RBM8A, LIX1L, GNRHR2, POLR3GL, PEX11B, TXNIP, PIAS3, NOTCH2NL, POLR3C, RNF115 ## NUDT4P1, GPR89A, SEC22B, PRKAB2, PDE4DIP, CHD1L, PFN1P2, BCL9, GPR89B, LINC00623 ## NBPF24, SRGAP2C, NBPF15, FCGR1B, NBPF16, FCGR1C, NOTCH2, FCGR1A, PHGDH, HIST2H2BF ##阴性:RIT1, SYT11, GON4L, KIAA0907, DAP3, YY1AP1, ARHGEF2, MSTO1, ASH1L, SSR2 ## RUSC1, FDPS, UBQLN4, CLK2, LAMTOR2, LRRC47, RPL22, DFFB, WRAP73, ICMT ## C1orf174, ACOT7, PANK4, LMNA, SCAMP3, PEX10, NOL9, KLHL21, THAP3, RER1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

阳性:PLEKHH2, DYNC2LI1, ZFP36L2, LRPPRC, THADA, PPM1B, MTA3, PREPL, COX7A2L, SRBD1 ## PIGF, EML4, CRIPT, SOCS5, MCFD2, SLC8A1, CALM2, BCYRN1, MSH2, MSH6 ## THUMPD2, FBXO11, RTN4, FOXN2, SPTBN1, RPS27A, ACYP2, PPP1R21, TMEM178A, NRXN1 ##阴性:USP40, DGKD, ATG16L1, INPP5D, GIGYF2, EFHD1, EIF4E2, TIGD1, DIS3L2, cops7bb# # PDE6D, PTMA, NCL, ARMC9, PSMD1, ITM2C, CAB39, SP100, SP110, FBXO36 ## TRIP12, DNER, PID1, SPHKAP, MFF, RHBDD1, DOCK10, CUL3, SERPINE2, MRPL44 ## pc2 ##阳性:BCS1L, ZNF142, RNF25, RQCD1, STK36, USP37, CTDSP1, TTLL4, SLC11A1, CYP27A1 ## TMBIM1, NHEJ1, PNKD, AAMP, ARPC2, CNPPD1, TNS1, RPL37A, FAM134A, SMARCAL1 ## ZFAND2B, XRCC5, TMEM169, ABCB6, PECR, ATG9A, ANKZF1, ATIC, DNAJB2, SPAG16 ##SFXN5, SMYD5, SPR, EXOC6B, ZNF638, PRADC1, MPHOSPH10, CCT7, MCEE, nagk# # ALMS1, TEX261, TPRKB, VAX2, DUSP11, ADD2, STAMBP, TGFA, DGUOK, fam136a# # BOLA3, PNO1, PPP3R1, PLEK, NFU1, GFPT1, wno1, LOXL3, MRPL19, HTRA2, AUP1, GCFC2, PCGF1, LRRTM4, CTNNA2 ## TTC31, CCDC142, SUCLG1, MRPL53, MOGS, TMSB10, WBP1, TGOLN2, RTKN, RETSAT ## WDR54, DCTN1, CAPG, MOB1A, MAT2A, BOLA3- as1, GGCX, BOLA3 ##阴性:CCDC115、IMP4、MZT2B、PTPN18、FAM168B、ARHGEF4、SMPD4、PLEKHB2、MZT2A、c2orf27a# # HS6ST1、CCNT2、NCKAP5、RAB3GAP1、R3HDM1、UBXN4、UGGT1、SAP130、AMMECR1L、POLR2D ## EPC2、KIF5C、MMADHC、WDR33、RND3、NMI、RIF1、gpr4、PDCL3、MRPS9、CHST10、GPR45、AFF3、C2orf49、NCK2 ## REV1、UXS1、EIF5B、ST6GAL2、GCC2、TXNDC9、LIMS1、MRPL30、RANBP2、SEPT10 ## MITD1、RGPD5、LINC00116、LIPT1、MERTK、MGAT4A、ZC3H8、TTL、POLR1B、CHCHD5 ##否定:RAB1A, ACTR2, SPRED2, CEP68, MEIS1, AFTPH, PELI1, UGP2, ETAA1, MDH1 ## C1D, WDPCP, WDR92, EHBP1, PNO1, B3GNT2, PPP3R1, CNRIP1, COMMD1, plek# # CCT4, ANTXR1, FAM161A, GFPT1, XPO1, NFU1, USP34, ANXA4, AHSA2, GMCL1 ## PC_ 5 ##阳性:BIN1, GYPC, ERCC3, CNTNAP5, MKI67IP, TSN, IWS1, CLASP1, LIMS2, POLR2D ## WDR33, AMMECR1L, GPR17, RALB, SAP130, EPB41L5, UGGT1, DBI, INSIG2, HS6ST1 ## CCDC93, SMPD4, DDX18, CBWD2, IL1A, IL1B, SLC20A1, ACTR3, CHCHD5, POLR1B ##阴性:Ucn, mpv17, cad, gtf3c2, atraid, eif2b4, snx17, slc5a6, ppm1g, preb# # nrbp1, cgref1, ift172, khk, znf512, ost4, ccdc121, agbl5, gpn1, tmem214 ## mapre3, supt7l, dpysl5, slc4a1ap, slc35f6, mrpl33, kcnk3, ept1, bre, hadhb

##计算最近邻图

计算SNN

##定心缩放数据矩阵

阳性:TMEM115, C3orf18, CYB561D2, HEMK1, NPRL2, MAPKAPK3, SEMA3B, IFRD2, RASSF1, GNAI2 ## MANF, TUSC2, HYAL2, NAT6, SLC38A3, VPRBP, RBM5, RAD54L2, RBM6, TEX264 ## MON1A, RRP9, UBA7, PARP3, GPR62, PCBP4, FAM212A, ABHD14B, IP6K1, ABHD14A ##阴性:ATP6V1A、NAA50、KIAA2018、MIR568、SPICE1、ZBTB20、GAP43、C3orf17、LSAMP、GTPBP8 ## SLC35A5、IGSF11、ATG3、B4GALT4、CD200、ARHGAP31、ABHD10、PVRL3、TMEM39A、DZIP3 ## POGLUT1、IFT57、TIMMDC1、CD47、BBX、COX17、XPC、TMEM43、CHCHD4、METTL6、HDAC11、EAF1、HACL1、IQSEC1 ## BTD、ANKRD28、GALNT15、RPL32、dph1、WDR48、CSRNP1、OXSM、CX3CR1 ## EXOG、OXNAD1、NKIRAS1、NGLY1、SLC4A7、SLC25A38、RPL15、UBE2E1、TOP2B、NR1D2 ##阴性:CHMP2B, CADM2, CGGBP1, GBE1, ZNF654, C3orf38, ROBO1, pro1, DHFRL1, FAM86DP ## NSUN3, PPP4R2, CLDND1, SHQ1, ST3GAL6, FOXP1, ARL6IP5, cmdnd1, TBC1D23, UBA3 ## NIT2, TMF1, TOMM70A, LNP1, SUCLG2, TMEM45A, TFG, KBTBD8, SENP7, LRIG1 ## pc3 ##阳性:RFT1, TKT, NEK4, DCP1A, CHDH, SPCS1, IL17RB, GLT8D1, ACTR8, GNL3 ## PBRM1, SELK, NT5DC2, ERC2, STAB1, CCDC66, NISCH, BAP1, FAM208A, GLYCTK ## WDR82, IL17RD, TWF2, APPL1, ALAS1, DUSP7, PDE12, RPL29, ARF4, ACY1 ##阴性:AZI2, STT3B, GPD1L, CMTM7, CMC1, CMTM6, SLC4A7, DYNC1LI1, CNOT10, OXSM ## GLB1, NGLY1, TMPPE, TOP2B, CRTAP, NR1D2, SUSD5, FBXL2, RPL15, CLASP2 ## PDCD6IP, ARPP21, NKIRAS1, EPM2AIP1, MLH1, UBE2E1, LRRFIP2, GOLGA4, WDR48, GORASP1, LRRFIP2, CSRNP1, MLH1, CX3CR1, SLC25A38, EPM2AIP1, RPSA, ARPP21, MOBP, EIF1B, PDCD6IP, CLASP2 ## RPL14, FBXL2, SUSD5, CRTAP, TMPPE, ZNF619, GLB1, CNOT10, DYNC1LI1, ZNF620 ##VPS8, MAGEF1, C3orf70, MAP3K13, POLR2H, FAM131A, TMEM41A, EIF4G1, SENP2, TRA2B ## PSMD2, ETV5, ECE2, DGKG, ALG3, TBCCD1, ABCF3, dnajb5, AP2M1, EIF4A2 ## DVL3, RFC4, ST6GAL1, EIF2B5, MASP1, ABCC5, BCL6, PARL, lif2b5, MASP1, ABCC5, BCL6, SEC13, TAMM41, IRAK2, VHL, TIMP4, TSEN2, BRK1 CIDECP, MKRN2, EMC3, CRELD1, RAF1, CAND2, JAGN1, RPL32, RPUSD3, IQSEC1 ## HDAC11, TTLL3, CHCHD4, ARPC4, TMEM43 ##阴性:Mylk, ccdc14, ptplb, sec22a, kalrn, sema5b, hspbap1, umps, dtx3l, znf148 ## parp9, snx4, osbpl11, kpna1, slc41a3, wdr5b, zxdc, fam162a, chchd6, ccdc58 ## plxna1, cd86, tpra1, slc15a2, McM2, iqcb1, podxl2, golgb1, mgll, hcls1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:FAM149A, UFSP2, ANKRD37, KIAA1430, SLC25A4, ACSL1, CASP3, IRF2, STOX2, TRAPPC11 ## RWDD4, ING2, CDKN2AIP, AGA, SPCS3, GPM6A, GLRA3, CEP44, FBXO8, SCRG1 ## TMEM184C, SLC10A7, PRMT10, C4orf48, LSM6, DCLK2, RPS3A, HMGB2, SH3D19, AADAT ##阴性:APBB2, SLC30A9, UCHL1, LIMCH1, TMEM33, PDS5A, ATP8A1, UBE2K, GUF1, GNPDA2 ## SMIM14, COMMD8, UGDH- as1, NFXL1, UGDH, FRYL, LIAS, OCIAD1, RPL9, DCUN1D4 ## RFC1, SGCB, KLF3, KLF3, FIP1L1, TMEM156, TLR1, SCFD2, KLF3, FIP1L1, PGM2 ## pc2 ##阳性:TMEM156, TLR1, KLHL5, KLF3, RFC1, LAP3, QDPR, TAPT1-AS1, PGM2, RPL9 ## MED28, FAM200B, PACRGL, DHX15, DCAF16, ANAPC4, RELL1, LCORL, RBPJ, FBXL5 ## LIAS, TBC1D19, ARAP2, CC2D2A, UGDH, RAB28, UGDH- as1, WDR1, ACOX3, SMIM14 ##阴性:CBR4, SPOCK3, CPE, SH3RF1, CLCN3, C4orf27, MSMO1, MFAP3L, AADAT ## HMGB2, TMEM192, SCRG1, FAM218A, FBXO8, MARCH1, CEP44, TMA16, GLRA3, NAF1 ## GPM6A, RAPGEF2, SPCS3, PPID, ETFDH, AGA, TMEM144, CDKN2AIP, GRIA2, pp2 ## pc3 ##阳性:HELQ, COQ2, MRPS18C, COPS4, FAM175A, ARHGAP24, MAPK10, THAP9, KLHL8, THAP9- as1 ## HSD17B11, NUDT9, SEC31A, SPARCL1, SPP1, SCD5, PKD2, PPM1K, PYURF, RASGEF1B, NAP1L5, MRPL1, FAM13A, CCNI, SNCA, FAM47E ##阴性:MFSD10, LRPAP1, RGS12, ADD1, TMEM128, TNIP2, LYAR, FAM193A, ZBTB49, NSG1 ## RNF4, STX18, CYTL1, MXD4, CRMP1, HAUS3, wbc1d14, TADA2B, GRPEL1, AFAP1, SH3TC1, ACOX3, WDR1 ## pc_4 ##阳性:EIF4E, METAP1, TSPAN5, ADH5, RAP1GDS1, LAMTOR3, PDLIM5, SMARCAD1, GRID2, SNCA ## FAM13A, NAP1L5, PIGY, HERC3, PYURF, PPM1K, PKD2, SPP1, SPARCL1, NUDT9 ## HSD17B11, ADD1, tnip10, RGS12, FAM193A, LRPAP1, RNF4, TMEM128, MXD4 ##阳性:CHIC2, PDGFRA, FIP1L1, SRD5A3, TMEM165, SCFD2, CLOCK, DANCR, EXOC1, SGCB ## AASDH, DCUN1D4, PPAT, OCIAD1, FRYL, PAICS, NFXL1, SRP72, COMMD8, GNPDA2 ## NOA1, GUF1, POLR2B, ATP8A1, SLC30A9, LPHN3, TMEM33, UBA6, LIMCH1, UCHL1 ## pc5 ##阳性:FAM149A, UFSP2, ANKRD37, KIAA1430, SLC25A4, ACSL1, CASP3, IRF2, STOX2, TRAPPC11 ## RWDD4, ING2, CDKN2AIP, AGA, SPCS3, GPM6A, GLRA3, CEP44, FBXO8, SCRG1 ## HMGB2, AADAT, MFAP3L, C4orf27, COX18, DCK, ANKRD17, MOB1B, IL8, GRSF1 ##阴性:Lsm6, slc10a7, tmem184c, prmt10, dclk2, rps3a, sh3d19, pet112, fbxw7, arfip1 ## trim2, kiaa0922, tlr2, plrg1, ctso, pdgfc, glrb, gria2, tmem144, etfdh ## ppid, rapgef2, naf1, tma16, lamtor3, adh5, march1, metap1, eif4e, fam218a

##计算最近邻图

计算SNN

##定心缩放数据矩阵

pc_1 ##阳性:BOD1, CPEB4, BNIP1, CREBRF, ATP6V0E1, RPL26L1, ERGIC1, DUSP1, FBXW11, NPM1 ## RANBP17, CCDC127, PANK3, AFF4, SDHA, RARS, LEAP2, MAT2B, UQCRQ, PDCD6 ## NUDCD2, 9月8日，KIF3A, RAD50, CCNG1, C5orf55, IRF1, GABRG2, C5orf56, EXOC3 ##阴性:COX7C, EDIL3, HAPLN1, RASA1, VCAN, CCNH, TMEM161B, XRCC4, TMEM161B- as1, LINC00461 ## MEF2C, TMEM167A, CETN3, RPS23, MBLAC2, ATG10, COL4A3BP, SSBP2, POLK, HMGCR ## ZCCHC9, POC5, ARRDC3, MSH3, MTRNR2L2, FAM169A, F2R, ZFYVE16, AGGF1, PDE8B ## pc2 ##阳性:PCDHB13, PCDHB12, PCDHB19P, PCDHB11, TAF7, PCDHB9, PCDHGB2, PCDHB16, PCDHGA7, PCDHB8 ## PCDHGB4, PCDHB7, PCDHGA10, ZMAT2, PCDHGB7, HARS2, PCDHGC3, PCDHGC4, HARS, HDAC3 ## PCDH1, KIAA0141, DND1, RNF14, GNPDA1, WDR55, NDFIP1, FGF1, NR3C1, IK ##DHX29, SKIV2L2, ARL15, NDUFS4, PPAP2A, MOCS2, PARP8, MRPS30, SLC38A9, NNT IL6ST, PAIP1, MIER3, C5orf28, HMGCS1, GPBP1, NIM1, PLK2, ERCC8, ZNF131 ## NDUFAF2, SMIM15, SEPP1, ZSWIM6, FBXO4, KIF2A, DIMT1, C5orf51, IPO11, OXCT1 ## pc3 ##阳性:FAM173B, CCT5, SEMA5A, cbll, FASTKD3, MARCH6, MTRR, DAP, SRD5A1, NSUN2 ## CTNND2, MED10, NDUFS6, TRIO, MRPL36, FAM105A, SDHAP3, ANKH, LPCAT1, clptm1l# # ZNF622, BRD9, MYO10, zdhhc55, TPPP, BASP1, EXOC3, GUSBP1, C5orf55, CDH10 ##阴性:RASA1, CCNH, COX7C, EDIL3, TMEM161B, HAPLN1, TMEM161B- as1, RPS23, ATG10, VCAN ## XRCC4, TMEM167A, LINC00461, SSBP2, ZCCHC9, MEF2C, MSH3, RIOK2, CETN3, LNPEP ## CAST, MBLAC2, ARRDC3, RIOK2, ELL2, MTRNR2L2, FAM172A, GLRX, TTC37, RGMB ## pc_4 ##阳性:SLC12A2, ISOC1, HINT1, PRRC1, LYRM7, PHAX, ALDH7A1, CDC42SE2, GRAMD3, RAPGEF6 ## ZNF608, FNIP1, CSNK1G3, ACSL6, SNX24, SLC22A5, SNX2, C5orf56, IRF1, SRFBP1 ## RAD50, HSD17B4, KIF3A, SEPT8, DMXL1, UQCRQ, SEMA6A, LEAP2, AFF4, COMMD10 ##阴性:CCNG1, GABRG2, SLU7, PWWP2A, NUDCD2, TTC1, MAT2B, UBLCP1, RNF145, RARS ## CLINT1, PANK3, RANBP17, THG1L, NPM1, CYFIP2, FBXW11, MED7, DUSP1, ERGIC1 ## HAVCR2, RPL26L1, ATP6V0E1, CREBRF, BNIP1, BOD1, CPEB4, DCTN4, RBM22, NDST1 ## PC_ 5 ##阳性:TTC37, RHOBTB3, FAM172A, GLRX, ARRDC3, ELL2, MBLAC2, CAST, CETN3, ERAP1 ## MEF2C, LNPEP, LINC00461, RIOK2, TMEM161B- as1, RGMB, TMEM161B, CHD1, CCNH, FAM174A ## NSUN2, MED10, SRD5A1, MRPL36, NDUFS6, SDHAP3, MTRR, LPCAT1, RASA1, FASTKD3 ##阴性:Smim15, ndufaf2, zswim6, ercc8, plk2, kif2a, gpbp1, dimt1, ipo11, mier3 ## rnf180, il6st, cwc27, slc38a9, ppwd1, ppap2a, trim23, skiv2l2, trappc13, dhx29 ## sgtb, arl15, nln, ndufs4, dnajc18, tmem173, mocs2, ube2d2, cxxc5, parp8

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:BAG2, PRIM2, ZNF451, GUSBP4, KIAA1586, KHDRBS2, BEND6, DST, PTP4A1, PHF3 ## GCLC, BAI3, ELOVL5, LMBRD1, ICK, FAM135A, GSTA4, C6orf57, SMAP1, tmem14a# # MTO1, EEF1A1, EFHC1, SLC17A5, COX7A2, PAQR8, TMEM30A, SENP6, MYO6, PHIP ##阴性:VARS, LSM2, MSH5, CLIC1, HSPA1A, DDAH2, ABHD16A, HSPA1B, LY6G5C, C6orf48 ## NELFE, SKIV2L, STK19, C2, EHMT2, NEU1, ATF6B, LY6G5B, PPT2, PPT2-EGFL8 ## EGFL8, CSNK2B, AGPAT1, GPANK1, HLA-DRA, C6orf47, HLA-DRB5, BAG6, HLA-DRB1, PRRC2A ## pc_2 ##阳性:PRDM1, PREP, ATG5, HACE1, GRIK2, ASCC3, RTN4IP1, CCNC, PNISR, QRSL1 ## COQ3, FBXL4, C6orf203, POU3F2, PDSS2, KLHL32, SEC63, NDUFAF4, OSTM1, UFL1 ## SNX3, FOXO3, FUT9, MANEA, SESN1, MAP3K7, CEP57L1, CASP8AP2, CD164, MICAL1 ##阴性:CAHM, AGPAT4, QKI, MAP3K4, SFT2D1, LPAL2, MPC1, RPS6KA2, MRPL18, RNASET2 ## TCP1, FGFR1OP, ACAT2, MLLT4, THBS2, WTAP, SOD2, C6orf120, TAGAP, LINC00574 ## EZR, DLL1, DYNLT1, FAM120B, TMEM181, PSMB1, TULP4, TBP, PDCD2, SERAC1 ## PC_ 3 ##阳性:GMNN, C6orf62, HIST1H1C, HIST1H4C, ACOT13, ALDH5A1, TDP2, GPLD1, MRS2, NRSN1 ## HIST1H2BC, SOX4, CDKAL1, HIST1H2AC, MBOAT1, HIST1H1E, DEK, HIST1H2BD, TPMT, hist1h4e# # KIF13A, HIST1H2BG, BTN3A2, NUP153, BTN3A1, BTN3A3, BTN2A1, HMGN4, FAM8A1, ABT1 ##PEX7, BCLAF1, AHI1, IFNGR1, TNFAIP3, HBS1L, SGK1, HMGA1P7, KIAA1244, TBPL1 ## NHSL1, RPS12, CCDC28A, ABRACL, CITED2, AKAP7, FUCA2, LTV1, EPB41L2, SF3B5, PTPRK, FBXO30, SHPRH ## PC_ 4 ##阳性:NHSL1, CCDC28A, KIAA1244, ABRACL, TNFAIP3, CITED2, IFNGR1, PEX3, VTA1, AIG1 ## PEX7, FUCA2, BCLAF1, LTV1, AHI1, HBS1L, SF3B5, FBXO30, SGK1, SHPRH ## HMGA1P7, TBPL1, SASH1, RPS12, UST, SLC18B1, PHACTR1, NEDD9, TBC1D7, SIRT5 ##阴性:PPP2R5D, MEA1, CNPY3, KLHDC3, C6orf226, KLC4, RPL7L1, TBCC, UBR2, TRERF1 ## NFYA, TREM2, MRPS10, TREM1, MED20, BYSL, TAF8, SAYSD1, GLO1, BTBD9, ZFAND3, CCDC167, RNF8, PIM1, FGD2, CCDC167, RNF8, PIM1, FGD2, AGPAT4, MAP3K4, RNASET2, LPAL2, MRPL18 ## FGFR1OP, TCP1, ACAT2, MLLT4, TMEM181, WTAP, TULP4, DYNLT1, TAGAP, SOD2 ## EZR, SERAC1, THBS2, TMEM242, ARID1B, C6orf120, TFB1M, LINC00574, SCAF8, DLL1 ##负:SRSF3, CDKN1A, PPIL1, STK38, C6orf89, KCTD20, MTCH1, FGD2, BRPF3, PIM1 ## SRPK1, RNF8, FKBP5, CCDC167, ZFAND3, RPL10A, BTBD9, PPARD, GLO1, DEF6 ## SAYSD1, ZNF76, MOCS1, OARD1, TAF11, NFYA, UHRF1BP1, TREM2, SNRPC, TREM1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

PC_ 1 ##阳性:PDK4, PPP1R9A, DYNC1I1, PON2, PEG10, SLC25A13, SGCE, SHFM1, CASD1, BET1 ## ACN9, CCDC132, ASNS, FAM133B, LMTK2, RBM48, TECPR1, PEX1, GATAD1, BRI3 ## ANKIB1, KRIT1, TMEM130, CROT, CYP51A1, TP53TG1, SLC25A40, DBF4, AKAP9 ##阴性:CUL1, FAM115A, CNTNAP2, EZH2, ZYX, PDIA4, FAM131B, ZNF425, ZNF282, CASP2 ## GSTK1, ZNF212, MTRNR2L6, ZNF767, SSBP1, KIAA1147, ATP6V0E2, H2AFV, PPIA, TRIL ## AGK, MRPS33, ZMIZ2, CREB5, BRAF, OGDH, REPIN1, NDUFB2, JAZF1, TMED4 ## pc2 ##阳性:SLC25A13, DYNC1I1, BRAF, OGDH, REPIN1, NDUFB2, TECPR1, ACN9, ASNS, LMTK2, PON2, TECPR1, ppp1r9abri3, PEG10, TMEM130, SGCE, ARPC1A, CASD1, ARPC1B, BET1, PDAP1, CCDC132 ## FAM133B, BUD31, RBM48, PTCD1, PEX1, GATAD1, CPSF4, ANKIB1, ATP5J2, KRIT1 ##阴性:PHF14, NDUFA4, NXPH1, THSD7A, TMEM106B, ICA1, GLCCI1, SCIN, RPA3, ARL4A ## MIOS, C1GALT1, CCZ1B, ETV1, ZDHHC4, KDELR2, DGKB, DAGLB, ANKMY2, RAC1 ## BZW2, FAM220A, TSPAN13, USP42, SNX13, EIF2AK1, HDAC9, AIMP2, TNPO3, AHCYL2 ## PC_ 3 ##阳性:FAM220A, USP42, AIMP2, EIF2AK1, HDAC9, AIMP2, PMS2, RNF216, RAC1, FSCN1, DAGLB ## ACTB, KDELR2, ZDHHC4, WIPI2, CCZ1B, C1GALT1, RNF216P1, MIOS, MMD2, RPA3 ## AP5Z1, GLCCI1, FOXK1, ICA1, GNA12, NXPH1, AMZ1, NDUFA4, TTYH3, PHF14 ##阴性:TMEM140, WDR91, C7orf49, CNOT4, CALD1, NUP205, BPGM, C7orf73, MTPN, AKR1B1 ## LUZP6, SLC35B4, PTN, EXOC4, DGKI, CHCHD3, CREB3L2, PODXL, TRIM24, MKLN1 ## ZC3HAV1, COPG2, UBN2, MEST, C7orf55, CEP41, LUC7L2, HIPK2, KLHDC10 ## PC_ 4 ##阳性:spdy8p, STAG3L3, NSUN5, NSUN5P2, POM121, BAZ1B, spdy7p, BCL7B, SBDSP1, STAG3L4 ## PMS2P4, TYW1, SBDS, TMEM248, RABGEF1, KCTD7, LINC00174, TPST1, CRCP, asl# # GUSB, VKORC1L1, CCT6P1, ZNF92, CCT6P3, ERV3-1, ZNF117, ZNF138, ZNF107, ZNF680 ##阴性:ZSCAN25, TRIM4, ZNF655, ZSCAN21, FAM200A, ZKSCAN5, AZGP1, ZKSCAN1, ZNF394 COPS6, ZNF789, MCM7, AP4M1, ATP5J2, TAF6, CNPY4, CPSF4, LAMTOR4, PTCD1 ## GAL3ST4, BUD31, GPC2, PDAP1, ARPC1B, GATS, ARPC1A, PVRIG, PMS2P1, TMEM130 ## pc5 ##阳性:GNAI1, MAGI2- as3, MAGI2, CACNA2D1, PHTF2, GRM3, TMEM60, DMTF1, RSBN1L, RSBN1L- as1 ## TMEM243, PTPN12, TP53TG1, POMZP3, CROT, DTX2, SLC25A40, DBF4, YWHAG, ADAM22 ## HSPB1, MDH2, SRI, STYXL1, STEAP2, CLDN12, MTERF, AKAP9, ARF5, GCC1 ##阴性:Prkag2, nub1, rheb, galnt11, abcf2, paxip1, dpp6, insig1, agap3, rbm33 ## tmub1, lmbr1, fastk, dnajb6, ptprn2, cdk5, esyt2, abcb8, wdr60, linc00689 ## kcnh2, vipr2, tmem176b, gimap2, gimap4, repin1, atp6v0e2, znf767, znf212, znf282

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:JRK, ARC, tssnare1, DENND3, PTK2, CHRAC1, TRAPPC9, KHDRBS3, NDRG1, SLA ## PHF20L1, EFR3A, ASAP1, FAM49B, MYC, FAM84B, TRIB1, NSMCE2, KIAA0196, SQLE ## MTSS1, NDUFB9, TATDN1, RNF139, TRMT12, DECR1, NBN, RIPK2, TMEM55A, FAM91A1 ##阴性:BNIP3L、PPP2R2A、PNMA2、ADAM28、SLC25A37、DPYSL2、ENTPD4、R3HCC1、CHMP7、ADRA1A ## TNFRSF10B、RHOBTB2、EGR3、STMN4、BIN3、TRIM35、PDLIM2、PTK2B、SORBS3、CLU ## PPP3CC、SCARA3、SLC39A14、CCDC25、POLR3D、ELP3、REEP4、FZD3、FAM160B2、XPO7 ## pc2 ##阳性:CPNE3、REXO1L1、MMP16、CA2、RIPK2、C8orf59、NBN、ZFAND1、DECR1、IMPA1 ## TMEM55A、PMP2、OTUD6B、FABP5、RUNX1T1、PAG1、TRIQK、ZNF704、FAM92A1、TPD52 ## MRPS28、RBM12B、HEY1、STMN2、PDP1、ZC2HC1A、KIAA1429、DPY19L4、INTS8、CCNE2 ##CLN8, ERICH1, FBXO25, CSMD1, ZNF596, MCPH1, AGPAT5, ERI1, TNKS, MSRA PINX1, CTSB, MTMR9, ZDHHC2, MSR1, NEIL2, FDFT1, TUSC3, CNOT7, vps37a# # MTMR7, MTUS1, PCM1, ASAH1, PSD3, CSGALNACT1, INTS10, LPL, atah1, PSD3, CSGALNACT1, INTS10, LPL, ATP6V1B2, FAM84B, MTSS1, NDUFB9, MYC, TATDN1, fam49b# # RNF139, ASAP1, TRMT12, EFR3A, FAM91A1, WDYHV1, PHF20L1, ZHX1, SLA, C8orf76 ## NDRG1, DERL1, KHDRBS3, ZHX2, TRAPPC9, CHRAC1, PTK2, DENND3, tssnare1, ARC ##阴性:PPAPDC1B, WHSC1L1, FGFR1, DDHD2, RNF5P1, BAG4, LSM1, ASH2L, BRF2, EIF4EBP1 ## PROSC, DUSP26, ERLIN2, UBE2V2, RPS20, RNF122, TGS1, CHCHD7, PCMTD1, TMEM68 ## MAK16, MRPL15, TTI2, RB1CC1, IMPAD1, LYPLA1, FUT10, ATP6V1H, TCEA1, FAM110B ## pc4 ##阳性:CPNE3, MMP16, REXO1L1, RIPK2, NBN, CA2, DECR1, C8orf59, TMEM55A, ZFAND1 ## OTUD6B, IMPA1, RUNX1T1, PMP2, CTSB, TRIQK, TUSC3, FDFT1, FABP5, NEIL2 ## MSR1, ZDHHC2, MTMR9, PINX1, FAM92A1, CNOT7, PAG1, MSRA, TNKS, RBM12B ##阴性:RNF5P1, FGFR1, WHSC1L1, PPAPDC1B, DDHD2, BAG4, LSM1, ASH2L, EIF4EBP1, BRF2 ## PROSC, ERLIN2, DUSP26, RNF122, MAK16, TTI2, FUT10, PPP2CB, UBE2V2, UBXN8 ## PCMTD1, GSR, RB1CC1, SMIM18, ATP6V1H, DCTN6, TCEA1, LYPLA1, LEPROTL1, MRPL15 ## pc5 ##阳性:SDCBP, UBXN2B, NSMAF, FAM110B, IMPAD1, TOX, CHCHD7, CA8, RPS20, RAB2A ## TGS1, CHD7, TMEM68, CLVS1, MRPL15, LYPLA1, TCEA1, ATP6V1H, RB1CC1, PCMTD1 ## UBE2V2, ZNF596, FBXO25, ERICH1, CLN8, CSMD1, AGPAT5, ERI1, TNKS ##阴性:Fzd3, extl3, elp3, ints9, ccdc25, scara3, clu, hmbox1, ptk2b, kif13b# # trim35, tmem66, stmn4, leprotl1, adra1a, dctn6, dpysl2, smim18, pnma2, GSR ## bnip3l, ubxn8, ppp2r2a, ppp2cb, adam28, fut10, ptdss1, cpq, mterfd1, uqcrb

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:GPSM1, PMPCA, NACC2, UBAC1, SEC16A, CAMSAP1, NOTCH1, MRPS2, PPP1R26, OLFM1 ## SNHG7, TMEM141, WDR5, PHPT1, BRD3, EDF1, TRAF2, LINC00094, FBXW5, PTGDS ## VAV2, ADAMTSL2, SLC2A6, REXO4, CACFD1, SURF4, SURF2, SURF1, RPL7A, MED22 ##阴性:TBC1D2, TRIM14, TGFBR1, NANS, ALG2, ANP32B, C9orf156, SEC61B, XPA, NCBP1 ## NR4A3, TSTD2, TMOD1, ZNF510, STX17, CDC14B, ERCC6L2, ERP44, LINC00476, PTCH1 ## INVS, C9orf3, TEX10, HIATL1, MSANTD3, PHF2, MSANTD3- tmeff1, FAM120A, LPPR1, MRPL50 ## pc2 ##阳性:ASTN2, TRIM32, ATP6V1G1, POLE3, CDK5RAP2, ALAD, MEGF9, PRPF4, CDC26, SLC31A1 ## FKBP15, SLC31A2, PSMD5, ZFP37, SNX30, ZNF883, INIP, HSDL2, PTBP3, UGCG ## RAB14, GNG10, ZNF483, GSN, KIAA0368, LPAR1, TXN, TMEM245, CTNNAL1, APTX, NFX1, NDUFB6, NOL6, TOPORS ## UBE2R2, DDX58, UBAP2, ac1, DCAF12, C9orf72, UBAP1, MOB3B, NUDT2, IFT74 ## KIAA1161, PLAA, FAM219A, CAAP1, RPP25L, CDKN2A, DCTN3, SIGMAR1, MTAP, galt# # pc_3 ##阳性:SURF1, RPL7A, SURF2, SURF4, MED22, REXO4, SURF6, CACFD1, GBGT1, SLC2A6 ## ADAMTSL2, RALGDS, VAV2, GTF3C5, LINC00094, TSC1, BRD3, WDR5, C9orf9, OLFM1 ## TTF1, PPP1R26, MRPS2, SETX, CAMSAP1, UBAC1, MED27, NACC2, UCK1, GPSM1 ##阴性:C9orf156, XPA, ANP32B, NCBP1, TSTD2, TMOD1, ZNF510, NANS, CDC14B, ERCC6L2 ## LINC00476, TRIM14, PTCH1, C9orf3, TBC1D2, HIATL1, PHF2, TGFBR1, FAM120A, ALG2 ## FAM120AOS, SEC61B, NR4A3，忍1,STX17, SUSD3, er61b, FGD3, INVS, TEX10 ## pc4 ##阳性:FAM122A, CBWD3, FXN, CBWD5, APBA1, SMC5, C9orf85, CBWD6, rfand5, PRUNE2, IGFBPL1, GNAQ, CEP78, ALDH1B1, PSAT1, SLC25A51 IDNK, UBQLN1, EXOSC3, HNRNPK, RMI1, TRMT10B, NTRK2, TOMM5, AGTPBP1, FBXO10 ##阴性:RANBP6, IL33, KIAA2026, UHRF2, PLGRKT, KDM4C, JAK2, PTPRD, MPDZ, RCL1 ## NFIB, AK3, ZDHHC21, CDC37L1, PPAPDC2, SNAPC3, RFX3, PSIP1, KIAA0020, SMARCA2 ## CNTLN, KANK1, RRAGA, DOCK8, HAUS6, CBWD1, PLIN2, DENND4C, RPS6, SLC24A2 ## pc5 ##阳性:CBWD1, DOCK8, KANK1, SMARCA2, KIAA0020, RFX3, PPAPDC2, CDC37L1, AK3, RCL1 ## JAK2, PLGRKT, KIAA2026, RANBP6, IL33, BICD2, ZNF484, uhrkt, IPPK, FGD3 ## NOL8, SUSD3, NINJ1, IARS, FAM120AOS, KDM4C, FAM120A, SCAI, PPP6C, MIR181A2HG, RABEPK, PSMB7, HSPA5, NEK6 ## DENND1A, RABGAP1, ZBTB26, ZBTB6, RC3H2, PDCL, MRRF, RBM18, PSMD5, MEGF9, CDK5RAP2, TRIM32, CCDC107, TLN1, RUSC2, CREB3, ASTN2

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:MTG1, ECHS1, ZNF511, TUBGCP2, INPP5A, LRRC27, DPYSL4, BNIP3, PPP2R2D, GLRX3 ## CDC123, PTPRE, CAMK1D, SEPHS1, DOCK1, PRPF18, FRMD4A, C10orf90, FAM107B, HSPA14 ## BCCIP, SUV39H2, DCLRE1C, UROS, RPP38, NMT2, FAM171A1, C10orf137, FAM188A, RSU1 ##阴性:SLC29A3, PCBD1, PALD1, EIF4EBP2, SGPL1, C10orf54, PPA1, SAR1A, PSAP, TYSND1 ## CHST3, TSPAN15, ASCC1, ANAPC16, HK1, DDIT4, SUPV3L1, DNAJB12, MICU1 ## MCU, SRGN, P4HA1, KIAA1279, ECD, DDX21, DNAJC9, DDX50, ECD, DDX21, DNAJC9, DDX50, BMS1, ZNF485, ZNF33B, ZNF37BP, HSD17B7P2, ZNF37A, ZNF33A ## ZNF32, ZNF25, ZNF248, CXCL12, CCNY, RASSF4, CREM, ZNF22, CUL2, ALOX5 ## FAM21C, NRP1, AGAP4, ITGB1, BMS1P1, EPC1, GLUD1P7, KIF5B, ARHGAP12, BMS1P2CCSER2, RGR, GRID1, CDHR1, WAPAL, GHITM, BMPR1A, GLUD1, TSPAN14, FAM213A ## FAM35A, TMEM254, MINPP1, ZCCHC24, ATAD1, PPIF, PTEN, ZMIZ1, RPS24, STAMBPL1 ## POLR3A, ACTA2, DLG5, KCNMA1, FAS, VDAC2, CH25H, LIPA, SAMD8, IFIT2 ## pc3 ##阳性:GSTO1, SFR1, ITPRIP, XPNPEP1, PDCD11, ADD3, MXI1, USMG5, SMNDC1, SMC3 ## PCGF6, PDCD4, INA, NT5C2, BBIP1, AS3MT, SHOC2, ZDHHC6, C10orf32, VTI1A ## WBP1L, TCF7L2, SFXN2, DCLRE1A, ARL3, NHLRC2, FAM160B1, TRIM8, TRUB1, ACTR1A ##阴性:MCU, MICU1, DNAJB12, P4HA1, ECD, DDIT4, DNAJC9, MRPS16, ANAPC16, ANXA7 ## MTRNR2L5, PCDH15, PPP3CB, ZWINT, CSTF2T, ASCC1, CISD1, sstf2t, USP54, BMS1P4 ## FAM21A, AGAP5, SEC24C, FUT11, UBE2D1, KAT6B, AGAP6, CHCHD1, CHST3, AGAP6, CHCHD1, FUT11, UBE2D1, KAT6B, AGAP6, CHCHD1, CHST3, BLOC1S2, CWF19L1, HIF1AN, CHUK, ERLIN1, fam178a# # DNMBP, COX15, MRPL43, CUTC, SLC25A28, LZTS2, GOT1, SFXN3, HPS1, MORN4, MMS19, ZDHHC16, LDB1, EXOSC1, PPRC1 ##阴性:CHST15, BUB3, OAT, ACADSB, LHPP, IKZF5, FAM53B, METTL10, PSTK, C10orf88 ## FAM175B, HTRA1, CTBP2, PLEKHA1, C10orf137, TACC2, UROS, NSMCE4A, BCCIP, ATE1 ## C10orf90, WDR11, DOCK1, PTPRE, PPAPDC1A, GLRX3, SEC23IP, PPP2R2D, BNIP3, MCMBP ## PC_ 5 ##阳性:OTUD1, MSRB2, ARHGAP21, PIP4K2A, PRTFDC1, COMMD3- bmi1, COMMD3, THNSL1, DNAJC1, NEBL ## PLXDC2, GPR158, ARL5B, NSUN6, STAM, APBB1IP, RSU1, FAM171A1, PDSS1 ## NMT2, RPP38, ABI1, DCLRE1C, ANKRD26, SUV39H2, HSPA14, YME1L1, FAM107B, ACBD5 ## Negative: DNAJC12, SIRT1, LRRTM3, HERC4, CTNNA3, PBLD, HNRNPH3, RUFY2, REEP3, SLC25A16 ## JMJD1C, TET1, NRBF2, CCAR1, EGR2, DDX50, ZNF365, DDX21, ARID5B, KIAA1279 ## ANK3, SRGN, CCDC6, VPS26A, FAM13C, phyhil, SUPV3L1, TFAM, HK1, UBE2D1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

阳性:MRPL48, COA4, RAB6A, PLEKHB1, STARD10, FAM168A, ATG16L2, PAAF1, RELT, FCHSD2 ## UCP2, C2CD3, PPME1, PGM2L1, POLD3, XRRA1, SPCS2, SLCO2B1, RPS3, B3GAT1 ## ACAD8, THYN1, VPS26B, NCAPD3, JAM3, IGSF9B, NTM, SNX19, ZBTB44, PHRF1 ##CD82, EXT2, ALKBH3, TP53I11, SLC35C1, CRY2, HSD17B12, MAPK8IP1, PEX16, phf21attc17, MDK, AMBRA1, HARBI1, API5, ATG13, LRRC4C, ARHGAP1, C11orf74, ZNF408 TRAF6, CKAP5, COMMD9, LRP4, LDLRAD3, TRIM44, C11orf49, SLC1A2, apaf6, C11orf49, LRP4, LDLRAD3, TRIM44, HEPACAM, SCN3B, GRAMD1B, HEPN1, HSPA8, SLC37A2, SORL1, FEZ1, TMEM136, EI24, PVRL1, STT3A, PUS3, THY1, DDX25, USP2 ## RPUSD4, RNF26, FAM118B, SRPR, MCAM, FOXRED1, CBL, TIRAP, dps, HINFP ##SVIP, FANCF, LUZP2, PRMT3, FIBIN, LIN7C, HTATIP2, BDNF-AS, NAV2- as5, NAV2 ## ZDHHC13, COPB1, METTL15, PSMA1, FAR1, TMEM86A, BTBD10 ## UEVLD, ARL14EP, C11orf58, TSG101, RPS13, NUCB2, SAAL1, PIK3C2A, HPS5, RPS13, GTF2H1, C11orf58, LDHA ## TSG101, SOX6, UEVLD, CYP2R1, SPTY2D1, TMEM86A, ZDHHC13, PSMA1, NAV2, COPB1 ## NAV2- as5, FAR1, HTATIP2, BTBD10, ARNTL, PRMT3, TEAD1, FANCF, PARVA, SVIP ##负:PICALM, EED, C11orf73, ME3, TMEM135, CTSC, CHORDC1, SLC36A4, TAF1D, C11orf54 ## MED17, PANX1, ANKRD49, CWC15, SRSF8, RPS3, ENDOD1, FAM76B, SLCO2B1, CEP57 ## SPCS2, MTMR2, MAML2, XRRA1, CCDC82, POLD3, JRKL, PGM2L1, CCDC82, SLC35F2, ELMOD1, ATM, CWF19L2, DDX10, AASDHPPT, RDX ## mantd4, FDX1, GRIA4, CASP1, LAYN, CASP4, SIK2, TMEM123, PPP2R1B, BIRC2 ## JRKL, ALG9, CCDC82, C11orf1, MAML2, CRYAB, MTMR2, CEP57, DIXDC1, FAM76B ##FADS1, BEST1, FTH1, FADS2, ASRGL1, FEN1, EEF1G, TUT1, TMEM258, MTA2 ## MYRF, B3GAT3, GANAB, INTS5, C11orf48, SDHAF2, C11orf83, CPSF7, UBXN1, TMEM216 ## BSCL2, TMEM138, TTC9C, DAK, ZBTB3, POLR2G, TAF6L, TMEM223, TMEM179B, TAF6L, t53i11, LRRC4C, SLC35C1, C11orf74 ## CRY2, TRAF6, MAPK8IP1, PEX16, COMMD9, PHF21A, MDK, LDLRAD3, AMBRA1, TRIM44 ## HARBI1, ATG13, SLC1A2, arhgap4, APIP, C11orf49 ## Negative:Cars, osbpl5, nap1l4, znf195, nup98, pgap2, kcnq1ot1, rhog, tssc4, stim1 ## cd81, rrm1, mrpl23, trim68, ctsd, trim22, ifitm10, mob2, fam160a2, tollip ## smpd1, chid1, polr2l, apbb1, cd151, trim3, pnpla2, rplp2, arfip2, pidd

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:KDM5A, NINJ2, WNK1, RAD52, ZCCHC8, ERC1, CLIP1, ADIPOR2, VPS33A, DCP1B ## DIABLO, FKBP4, MLXIP, ITFG2, NRIP2, BCL7A, RHNO1, PSMD9, TULP3, KDM2B ## PARP11, RNF34, CCND2, ANAPC5, C12orf5, CAMKK2, C12orf4, P2RX4, DYRK4, P2RX7 ##阴性:GLIPR1, KRR1, PHLDA1, NAP1L1, GLIPR1L2, ATXN7L3B, BBS10, TBC1D15, RAB21, OSBPL8 ## TMEM19, ALKBH2, SVOP, ZFC3H1, PPFIA2, CCDC59, MVK, CORO1C, SLC2A3, TMEM19, THAP2, CNOT2, ZFC3H1, LGR5, C3AR1, RAB21 ## RAB3IP, NECAP1, TBC1D15, CCT2, ATXN7L3B, CLEC4A, FRS2, GLIPR1L2, FAM66C, KRR1, LYZ, PHC1, PHLDA1, PTMS, NAP1L1, CPSF6, M6PR ##阴性:WSB2, RFC5, VSIG10, FBXO21, PEBP1, FBXW8, TAOK3, RNFT2, MAP1LC3B2, SUDS3 ## MED13L, PRKAB1, CIT, GCN1L1, PLBD2, RPLP0, PXN- as1, TPCN1, C12orf52, pxnddx54, COX6A1, RASAL1, TRIAP1, OAS1, GATC, SRSF9, RPH3A, DYNLL1, TNFRSF1A, IFFO1, CD9, NOP2, NDUFA9 ## DYRK4, CHD4, C12orf4, LPAR5, C12orf5, CCND2, ING4, PARP11, ZNF384, TULP3 ## RHNO1, COPS7A, NRIP2, MLF2, ITFG2, FKBP4, PTMS, DCP1B, ADIPOR2, ERC1 ##阴性:CHST11, SLC41A2, C12orf45, TXNRD1, ALDH1L2, KIAA1033, NFYB, HCFC2, APPL2, TDG ## C12orf75, C12orf73, HSP90B1, CKAP4, NT5DC3, TCP11L2, ASCL1, POLR3B, RIC8B, NUP37 ## C12orf23, MTERFD3, CCDC53, CRY1, PWP1, GNPTAB, CMKLR1, FICD, ARL1, SART3 ## PC_ 4 ##阳性:MTERFD3, C12orf23, CRY1, RIC8B, PWP1, POLR3B, CMKLR1, TCP11L2, FICD, CKAP4 ## SART3, C12orf75, ISCU, TMEM119, APPL2, SELPLG, CORO1C, KIAA1033, SSH1, ALDH1L2 ## SVOP, C12orf45, USP30, SLC41A2, ALKBH2, CHST11, UNG, TXNRD1, KCTD10, NFYB ##阴性:CTDSP2, TSFM, USP15, METTL1, CDK4, MON2, TSPAN31, PPM1H, OS9, B4GALNT1 ## DTX3, TMEM5, PIP4K2C, SRGAP1, KIF5A, C12orf66, DCTN2, XPOT, TBK1, DDIT3 ## GNS, MARS, LEMD3, LLPH, ARHGAP9, TMBIM4, R3HDM2, CAND1, SHMT2, DYRK2 ## pc_5 ##阳性:R3HDM2、ARHGAP9、SHMT2、LRP1、MARS、SNORA48、PRIM1、DDIT3、NACA、RAD52 ## WNK1、NINJ2、DCTN2、KDM5A、ERC1、ADIPOR2、KIF5A、DCP1B、PIP4K2C、FKBP4 ## DTX3、ITFG2、B4GALNT1、NRIP2、OS9、RHNO1、TSPAN31、TULP3、PARP11、DUSP16、LOH12CR1、LOH12CR2、MANSC1 ## UBE2N、LRP6、MRPL42、EEA1、BTG1、CRADD、ATP2B1、CCDC41、POC1B、magohb# # TMCC3、DUSP6、C12orf29、NDUFA12、KLRC2、CCDC59、NR2C1、PPFIA2、KLRC3、PPP1R12A

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc1 #阳性:DZIP1, ABCC4, DNAJC3, TGDS, SNORD22, UGGT2, SLITRK1, MBNL2, SPRY2, RAP2A ## NDFIP2, RBM26, IPO5, RNF219, DOCK9, EDNRB, UBAC2, SLAIN1, GPR183, MYCBP2 ## TM9SF2, FBXL3, PCCA, CLN5, TMTC4, KCTD12, NALCN, UCHL3, COMMD6, FGF14 ##阴性:FRY, N4BP2L1, p4bp2l2, PDS5B, RFC3, NBEA, SPG20, SMAD9, ALG5, EXOSC8 ## SUPT20H, UFM1, PROSER1, NHLRC3, LHFP, COG6, MRPS31, ELF1, WBP4, KBTBD6 ## KBTBD7, NAA16, RGCC, AKAP11, DNAJC15, ENOX1, ING1, CARKD, RAB20, IRS2 ## pc2 ##阳性:ALG5、SMAD9、SPG20、EXOSC8、NBEA、SUPT20H、RFC3、PDS5B、UFM1、N4BP2L2 ## PROSER1、N4BP2L1、NHLRC3、FRY、LHFP、COG6、MRPS31、WBP4、KBTBD7、NAA16、RGCC、AKAP11、DNAJC15、ENOX1、MRPS31P5、VPS36、CKAP2、HNRNPA1L2 ##否定:ABCC4、DZIP1、TGDS、DNAJC3、SNORD22、UGGT2、SLITRK1、MBNL2、RAP2A、SPRY2 ## IPO5、NDFIP2、DOCK9、UBAC2、RBM26、GPR183、TM9SF2、RNF219、PCCA、TMTC4 ## NALCN、FGF14、EDNRB、TPP2、TEX30、KDELC1、SLAIN1、BIVM、ERCC5、MYCBP2 ## pc_3 ##阳性:ING1, CARKD, RAB20, IRS2, MYO16, ABHD13, LIG4, ARGLU1, ERCC5, bivm# # KDELC1, TEX30, TPP2, FGF14, NALCN, TMTC4, PCCA, TM9SF2, GPR183, UBAC2 ## DOCK9, IPO5, FRY, N4BP2L1, N4BP2L2, PDS5B, RAP2A, RFC3, NBEA, SPG20 ##阴性:MRPS31P5, VPS36, CKAP2, HNRNPA1L2, SUGT1, PCDH17, TDRD3, PCDH9, MZT1, DIS3 ## PIBF1, KLF12, COMMD6, UCHL3, KCTD12, CLN5, EDNRB ## RNF219, RBM26, ENOX1, NDFIP2, DNAJC15, AKAP11, SLITRK1, NAA16 ## PC_ 4 ##阳性:ENOX1, DNAJC15, AKAP11, RGCC, NAA16, KBTBD7, ING1, KBTBD6, CARKD, RAB20 ## MRPS31P5, WBP4, IRS2, VPS36, MYO16, ABHD13, ELF1, CKAP2, LIG4, HNRNPA1L2 ## ARGLU1, MRPS31, SUGT1, ERCC5, BIVM, COG6, pcdh5, BIVM, COG6, PCDH17, PDS5B, RFC3, NBEA, SPG20, SMAD9, ALG5, SPRY2 ## SLITRK1, NDFIP2, SNORD22, RBM26, TGDS, ABCC4, RNF219, EDNRB ## UGGT2, SLAIN1, EXOSC8, MBNL2, MYCBP2, RAP2A, FBXL3, IPO5, CLN5, SUPT20H ## pc5 ##阳性:DZIP1, ABCC4, DNAJC3, TGDS, UGGT2, SNORD22, MBNL2, NAA16, SLITRK1, RGCC ## KBTBD7, RAP2A, AKAP11, SPRY2, KBTBD6, IPO5, DNAJC15, NDFIP2, WBP4, DOCK9 ## ENOX1, RBM26, UBAC2, ELF1, GPR183, RNF219, MRPS31, TM9SF2, COG6, IRS2, VPS36, MRPS31P5, CKAP2 ## HNRNPA1L2, MYO16, SUGT1, PDS5B, PCDH17, TDRD3, ABHD13, PCDH9, RFC3, MZT1 ## LIG4, DIS3, NBEA, ARGLU1, PIBF1, SPG20, ERCC5, KLF12, SMAD9, BIVM

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:METTL17, NDRG2, ARHGEF40, ZNF219, HNRNPC, SUPT16H, CHD8, RAB2B, TOX4, METTL3 ## SALL2, DAD1, ABHD4, OXA1L, MRPL52, LRP10, RBM23, PRMT5, HAUS4, PSMB5 ## ACIN1, C14orf119, PPP1R3E, C14orf80, BCL2L2-PABPN1, CRIP2, SLC22A17, PACS2, EFS, BRF1 ##阴性:SLC39A9, ERH, SMOC1, SRSF5, KIAA0247, EXD2, COX16, DCAF5, ZFP36L1, SYNJ2BP ## ZFYVE26, MED6, RDH11, PCNX, ZFYVE1, VTI1B, RBM25, PIGH, PSEN1, PLEKHH1 ## NUMB, ACOT2, PNMA1, EIF2S1, ELMSAN1, PTGR2, ATP6V1D, ZNF410, MPP5, FAM161B ## pc2 ##阳性:TMX1, TRIM9, GNG2, PYGL, C14orf166, TXNDC16, NIN, PSMC6, ATL1, styx# # MAP4K5, GNPNAT1, ATP5S, FERMT2, L2HGDH, DDHD1, ARF6, GMFB, NEMF, KLHDC2 ## KLHDC1, RPL36AL, MGAT2, DNAAF2, RPS29, CGRRF1, MDGA2, SOCS4, MIS18BP1, MAPK1IP1L ##阴性:SPATA7、ZC3H14、TTC8、GALC、FOXN3、SEL1L、EFCAB11、DIO2、PSMC1、NRXN3 ## CALM1、ADCK1、RPS6KA5、SNW1、C14orf159、SLIRP、SMEK1、TRIP11、ALKBH1、NDUFB1 ## SPTLC2、CPSF2、LGMN、AHSA1、GOLGA5、CHGA、VIPAS39、ITPK1、moap5、CMTM5、EFS、DHRS4- as1、DHRS4、SLC22A17 ## DHRS4L2、DCAF11、BCL2L2-PABPN1、PSME1、PPP1R3E、EMC9、C14orf119、PSME2、IRF9、ACIN1 ## REC8、PSMB5、IPO4、HAUS4、TM9SF1、PRMT5、RBM23、MDP1、LRP10 ##否定:LINC00643, PPP2R5E, SNAPC1, WDR89, HIF1A, SYNE2, SLC38A6, TRMT5, MTHFD1, MNAT1 ## ZBTB25, PPM1A, ZBTB1, DHRS7, HSPA2, PCNXL4, PLEKHG3, CHURC1, RTN1, CHURC1-FNTB ## FNTB, MAX, JKAMP, FUT8, L3HYPDH, GPHN, KIAA0586, MPP5, ATP6V1D, TIMM9 ## pc4 ##阳性:SLC25A29, WARS, YY1, WDR25, MEG3, DYNC1H1, PPP2R5C, EVL, HSP90AA1, EML1 ## WDR20, CINP, CYP46A1, TECPR2, CCNK, CDC42BPB, EIF5, SETD3, MARK3, CKB ## VRK1, TRMT61A, BAG5, PAPOLA, KLC1, APOPT1, INF2, C14orf2, ZFYVE21, GSKIP ##阳性:PSEN1、NUMB、RBM25、ACOT2、ZFYVE1、PCNX、PNMA1、MED6、ELMSAN1、SYNJ2BP ## PTGR2、COX16、ZNF410、SMOC1、SRSF5、FAM161B、KIAA0247、COQ6、SLC39A9、ALDH6A1 ## LIN52、ERH、ABCD4、EXD2、NPC2、DCAF5、ISCA2、ZFP36L1、FCF1、PLD4、APOPT1、CDCA4、KLC1、BRF1 ## PACS2、CRIP2、C14orf80、BAG5、TRMT61A、CKB、MARK3、EIF5、CDC42BPB、TECPR2 ## CINP、ZBTB1、HSPA2、ZBTB25、PLEKHG3、WDR20、MTHFD1、CHURC1、SYNE2、CHURC1- fntbMbip, linc00639, brms1l, sec23a, ralgapa1, gemin2, trappc6b, nfkbia, pnn, ctage5 ## psma6, klhl28, kiaa0391, fam179b, prpf39, ppp2r3c, fkbp3, fam177a1, ahsa1, sptlc2 ## vipas39, tmed8, alkbh1, mis18bp1, gstz1, slirp, snw1, pomt2, adck1, srp54

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:UBL7, SEMA7A, CLK3, PML, EDC3, STOML1, CSK, CD276, ULK3, NPTN ## NEO1, ADPGK, BBS4, ARIH1, HEXA, PARP6, PKM, SENP8, MYO9A, THAP10 ## LRRC49, LARP6, TLE3, RPLP1, ANP32A, CORO2B, FEM1B, CLN6, PIAS1, MAP2K5 ##阴性:RPAP1, TYRO3, VPS18, MGA, RTF1, ZFYVE19, CHP1, OIP5-AS1, NDUFAF1, MAPKBP1 ## DNAJC17, JMJD7, PLA2G4B, RMDN3, EHD4, VPS39, RPUSD2, TMEM87A, GANC, CAPN3 ## C15orf57, SNAP23, LRRC57, HAUS2, IVD, UBR1, TMEM62, CCNDBP1, KNSTRN, LCMT2 ## pc2 ##阳性:AKAP13, ZNF592, SEC11A, KLHL25, NMB, WDR73, NTRK3, ZSCAN2, MRPL46, UBE2Q2P1 ## MRPS11, DET1, SH3GL3, AEN, HDGFRP3, MFGE8, TM6SF1, ABHD2, BTBD1, POLG ## C15orf40, PEX11A, FAM103A1, AP3S2, WHAMM, C15orf38-AP3S2, C15orf38, CPEB1, IDH2, RPS17L ##阴性:OR4M2, TUBGCP5, CYFIP1, NIPA2, HERC2P2, HERC2P7, MKRN3, NDN, SNRPN, snurf3a, GABRB3, HERC2, HERC2P9, APBA2, TJP1, FAN1, MTMR10, SCG5, KNSTRN ## IVD, C15orf52, PLCB2, C15orf57, EMC7, SRP14, RPUSD2, f15orf61, CLN6, PIAS1, AAGAB, CORO2B, RPL4, ANP32A, SNAPC5 MAP2K1, RPLP1, TIPIN, DIS3L, MEGF11, RAB11A, LARP6, DENND4A, VWA9 ## LRRC49, PTPLAD1, DPP8, THAP10, PARP16, MYO9A, CLPX, SENP8, PDCD7, PKM ##阴性:NGRN, CRTC3, CIB1, IDH2, MAN2A2, UNC45A, HDDC3, C15orf38, VPS33B, CHD2 ## RGMA, IGF1R, C15orf38-AP3S2, LRRC28, AP3S2, MEF2A, PEX11A, LINS, POLG, ASB7 ## VIMP, ABHD2, SNRPA1, MFGE8, PCSK6, TM2D3, TARSL2, AEN, WASH3P, SPPL2A, DTWD1, GLDN, GALK2, COPS2, secisbp2l# # DMXL2, EID1, SHC4, SCG3, DUT, LYSMD2, MYEF2, TMOD2, GATM, MYO5A, SORD, B2M, SPG11, EIF3J, CTDSPL2 ##阴性:NDN、SNRPN、MKRN3、SNURF、HERC2P7、UBE3A、HERC2P2、GABRB3、NIPA2、HERC2 CYFIP1、TUBGCP5、HERC2P9、OR4M2、APBA2、TJP1、FAN1、MTMR10、SCG5、EMC7 ## PGBD4、KATNBL1、EMC4、NOP10、GOLGA8A、GOLGA8B、AQR、ZNF770、C15orf41、MEIS2 ## pc5 ##阳性:MORF4L1、CTSH、TMED3、ST20、BCL2A1、ZFAND6、ARNT2、MESDC2、EFTUD1、RPS17 ## UBE2Q2P3、RPS17L、CPEB1、WHAMM、FAM103A1、C15orf40、ULK3、CSK、BTBD1、EDC3 ## TMOD2、LEO1、LYSMD2、MAPK6、tmb5、MYO5A、CLK3、DMXL2 ##阳性:WASH3P, TARSL2, TM2D3, PCSK6, SNRPA1, VIMP, ASB7, LINS, MEF2A, LRRC28 ## IGF1R, RGMA, CHD2, VPS33B, HDDC3, UNC45A, MAN2A2, CRTC3, NGRN, MAP2K1 ## SNAPC5, TIPIN, RPL4, DIS3L, AAGAB, MEGF11, CIB1, RAB11A, C15orf61, DENND4A

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:ERVK13-1, PDPK1, ATP6V0C, AMDHD2, CEMP1, TBC1D24, KCTD5, SRRM2, ABCA3, TCEB2 ## FLYWCH2, rnqr4, E4F1, MLST8, HCFC1R1, TRAF7, THOC6 ## PKD1, ZNF200, TSC2, NTHL1, TIGD7, TBL3, ZNF75A, TSC2, NTHL1, FTO, SALL1, AKTIP, TOX3, FTO, SALL1, MMP2, CYLD, LPCAT2, NKD1 ## GNAO1, BRD7, AMFR, add7, CNEP1R1, ZNF423, SIAH1, LONP2, PHKB, ITFG1 ## DNAJA2, PLLP, CX3CL1, GPT2, CIAPIN1, COQ9, C16orf87, POLR2C, ORC6, GPR56 ## pc2 ##阳性:TCEB2, SRRM2, KCTD5, ERVK13-1, FLYWCH2, PDPK1, CEMP1, FLYWCH1, AMDHD2, atp6v0c# CFDP1, PAQR4, BCAR1, zfd7, ABCA3, TBC1D24, LDHD, GLG1, PSMD7, ABCA3, DHX38 ## FA2H, WDR59, HCFC1R1, TMEM170A, RNPS1, TXNL4B, ECI1, THOC6, DHODH, E4F1 ##阴性:FUS, KAT8, PYCARD, BCKDK, ITGAM, ITGAX, VKORC1, ARMC5, ZNF668, TGFB1I1 ## STX4, C16orf58, STX1B, ZNF267, ORAI3, HERC2P4, RNF40, VPS35, PHKG2, SRCAP ## ORC6, prr2, ZNF785, DNAJA2, ZNF688, ZNF764, ITFG1MGRN1, NUDT16L1, ANKS3, CDIP1, ZNF500, HMOX2, ROGDI, NMRAL1, DNAJA3, CORO7 ## CREBBP, PAM16, GLYR1, TRAP1, CLUAP1, NAGPA, NAA60, ZNF597, ALG1, ZNF174 ## FAM86A, MTRNR2L4, METTL22, ZNF75A, ABAT, TIGD7, TMEM186, ZNF200, PMM2, THOC6 ##阴性:FA2H, GLG1, PSMD7, WDR59, DHX38, LDHD, ZFP1, TXNL4B, DHODH, BCAR1 ## ZNF821, CFDP1, IST1, AP1G1, TMEM170A, ZNF19, TMEM231, ZNF23, GABARAPL2, HYDIN ## VAC14, ADAT1, MTSS1L, KARS, SF3B3, TERF2IP, COG4, DDX19A, MON1B, DDX19B ## pc4 ##阳性:PRKCB、TNRC6A、RBBP6、DCTN5、SLC5A11、PALB2、ARHGAP17、NDUFAB1、LCMT1、UBFD1 ## EARS2、NSMCE1、GGA2、GTF3C1、COG7、XPO6、SMG1P1、POLR3E、CLN3、EEF2K ## CCDC101、UQCRC2、EIF3C、RRN3P1、ATXN2L、IGSF6、TUFM、NFATC2IP、METTL9、SPNS1 ## Negative: AMFR、GNAO1、LPCAT2、MMP2、FTO、AKTIP、RBL2、CHD9、PLLP、CX3CL1 ## TOX3、CIAPIN1、COQ9、SALL1、POLR2C、GPR56、CYLD、KATNB1、NKD1、KIFC3 ## USB1、BRD7、C16orf80、ADCY7、CCDC113、NDRG4、CNEP1R1、SETD6、ZNF423、CNOT1 ## pc5 ## Positive:NUBP1, C16orf72, CLEC16A, USP7, LITAF, CARHSP1, PMM2, TMEM186, ABAT, METTL22 ## FAM86A, ALG1, NAGPA, GLYR1, ROGDI, ZNF500, ANKS3, NUDT16L1, MGRN1, CDIP1 ## HMOX2, NMRAL1, DNAJA3, CORO7, PAM16, CREBBP, TRAP1, CLUAP1, baa60, ZNF597 ##阴性:RPUSD1, NARFL, CHTF18, HAGHL, LMF1, FAM173A, SOX8, UBE2I, BAIAP3, gnptg# # UNKL, C16orf91, CLCN7, TELO2, CRAMP1L, MAPK8IP3, NME3, MRPS34, SPSB3, NUBP2 ## HAGH, FAHD1, MSRB1, NDUFB10, RPS2, SNHG9, TBL3, NTHL1, TSC2

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:LRRC37B, RHOT1, SUZ12, C17orf75, ZNF207, PSMD11, UTP6, TMEM98, CCL2, COPRS ## ZNF830, EVI2A, LIG3, RFFL, EVI2B, RAD51D, NLE1, OMG, AP2B1, CCL5 ## NF1, CCL3, CCL4, ADAP2, CCL3L3, TEFM, CCL4L1, CRLF3, CCL3L1, TEFM, CCL4L1, ANKRD40, KAT7, LUC7L3, SLC35B1 ## TOB1, SPAG9, NME1, SPOP, NME2, PHB, UTP18, ZNF652, SNF8, CA10 ## UBE2Z, COX11, ATP5G1, ATP1B2, SAT2, TP53, CALCOCO2, WRAP53, MMD ## pc2 ##阳性:TACO1, DCAF7, TANC2, STRADA, METTL2A, MED13, CCDC47, INTS2, DDX42, FTSJ3 ## BCAS3, PSMC5, PPM1D, TEX2, APPBP2, POLG2, USP32, DDX5, HEATR6, MIR3064 ## RNFT1, MIR5047, RPS6KB1, CEP95, TUBD1, SMURF2, VMP1, PTRH2, PLEKHM1P, CLTC ##阳性:PFN1, RNF167, SPAG7, CAMTA2, SLC25A11, ZFP3, PLD2, PSMB6, ZNF232, CXCL16 ## ZNF594, MED11, ARRB2, PELP1, RABEP1, MYBBP1A, NUP88, UBE2G1, ANKFY1, DERL2, ITGAE, MIS12, WSCD1, EMC6, TXNDC17 ## pc3 ##阳性:CA10, UTP18, COX11, MMD, NME2, TMEM100, PCTP, NME1, TRIM25, SPAG9 ##线圈，SCPEP1, TOB1, AKAP1, MSI2, LUC7L3, ankrd27, SPATA20 ## RSAD1, LRRC59, XYLT2, KAT7, PDK2, SLC35B1, SPOP, VEZF1, PHB, ZNF652 ##阴性:TP53I13, TAOK1, NUFIP2, GIT1, CORO6, TIAF1, ADAP2, TEFM, SSH2, CRLF3 ## NF1, LRRC37BP1, NSRP1, GOSR1, BLMH, OMG, MYO18A, EVI2B, EVI2A, SEZ6 ## COPRS, UTP6, PHF12, SUZ12, LRRC37B, FLOT2, RHOT1, C17orf75, ERAL1, ZNF207 ## PC_ 4 ##阳性:ZNHIT3, MYO19, CCL4L2, CCL3L1, PIGW, CCL4L1, GGNBP2, CCL3L3, AATF, CCL4 ## ACACA, TADA2A, PRKAR1A, ABCA8, CCL3, KCNJ16, SOX9, AMZ2, CCL5, COG1, SYNRG, FAM104A, AP2B1, KPNA2, NLE1, DRG2, PEMT, ALKBH5, RASD1, LLGL1 ## MED9, COPS3, FLII, FLCN, MPRIP, TOP3A, USP32P1, SMCR8, SHMT1 ## ZNF624, CCDC144B, ZNF287, TVP23B, C17orf76-AS1, PRPSAP2, UBB, EPN2, PIGL, EPN2- as1 ## pc5 ##阳性:C17orf80、FAM104A、CDC42EP4、RPL38、COG1、TTYH2、SSTR2、BTBD17、CD300A、SLC9A3R1、NAT9、SOX9、TMEM104、FDXR、KCNJ16、ABCA8、HID1、PRKAR1A、cdr2l# # AMZ2、ICT1、LINC00674、ATP5H、KPNA2、ARMC7、C17orf58、NT5C、BPTF、HN1 ##阴性:NPEPPS、KPNB1、CDC27、OSBPL7、GOSR2、MRPL10、NSF、SCRN2、PNPO、CDK5RAP3 ## ARL17A、NFE2L1、CBX1、LRRC37A2、SNX11、NSFP1、CALCOCO2、ATP5G1、ARL17B、ube2zsnf8、KANSL1- as1、ZNF652、KANSL1、MAPT、PHB、LRRC37A4P、SPOP、PLEKHM1、SLC35B1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:RPL17, RPL17-C18orf32, ACAA2, C18orf32, MBD1, DYM, CXXC1, CTIF, ME2, SMAD2 ## ELAC1, SMAD4, IER3IP1, DCC, HDHD2, POLI, PIAS2, C18orf54, C18orf25, TCF4 ## HAUS1, TXNL1, ATP5A1, WDR7, EPG5, SETBP1, ST8SIA3, PIK3C3, CELF4, FECH ##阴性:RIOK3, C18orf8, NPC1, TTC39C, CABYR, OSBPL1A, IMPACT, RBFA, TXNL4A, MBP, TSHZ1, SS18, CNDP1, CNDP2, CHST9, FAM69C, CDH2, CYB5A ## TIMM21, TRAPPC8, SOCS6, RTTN, RNF138, TMX3, DSEL, dtsna, CNDP1, CNDP2, FAM69C, cyb5, TIMM21 ## SOCS6, RTTN, TMX3, DSEL, SERPINB8, VPS4B, KDSR, PHLPP1, KIAA1468, PIGN ## CDH20, LMAN1, SEC11C, ZNF532, NARS, FECH, ST8SIA3, WDR7, TXNL1, TCF4 ##阴性:IMPACT, ZNF521, OSBPL1A, SS18, CABYR, CHST9, TTC39C, CDH2, NPC1, TRAPPC8 ## C18orf8, RNF138, RIOK3, dttna, MAPRE2, ZNF397, ZSCAN30, ZNF271, ZNF24, INO80C ## GALNT1, C18orf21, RPRD1A, SLC39A6, ELP2, TPGS2, KIAA1328, CELF4, PIK3C3, SETBP1 ## PC_ 3 ##阳性:DYM, C18orf32, CTIF, SMAD2, RPL17-C18orf32, RPL17, IER3IP1, ACAA2, HDHD2, MBD1 ## PIAS2, CXXC1, C18orf25, ME2, HAUS1, ELAC1, ATP5A1, SMAD4, EPG5, DCC ## SETBP1, POLI, PIK3C3, C18orf54, CELF4, TCF4, KIAA1328, TXNL1, TPGS2, WDR7 ##阳性:RIOK3, C18orf8, NPC1, TTC39C, CABYR, OSBPL1A, IMPACT, ZNF521, RBFA, SS18 ## TXNL4A, ATP9B, CNDP1, CHST9, CNDP2, FAM69C, CDH2, CYB5A ## TIMM21, SOCS6, TRAPPC8, RTTN, RTTN, TMX3, DSEL, RNF138, SERPINB8, VPS4B, TSHZ1, CNDP1, CNDP2, FAM69C, CYB5A, TPGS2 ## ELP2, KIAA1328, CELF4, SLC39A6, PIK3C3, RPRD1A, TIMM21, SETBP1, C18orf21, EPG5 ## GALNT1, ATP5A1, SOCS6, HAUS1, INO80C, C18orf25, RTTN, ZNF24, PIAS2, HDHD2 ##否定:FECH、ST8SIA3、NARS、WDR7、ZNF532、TXNL1、TCF4、SEC11C、C18orf54、RIOK3 ## C18orf8、LMAN1、POLI、NPC1、TTC39C、DCC、CABYR、CDH20、SMAD4、OSBPL1A ## IMPACT、ELAC1、PIGN、ZNF521、ME2、KIAA1468、SS18、ZNF271、LMAN1、ZNF24、ZSCAN30、SEC11C、PHLPP1、INO80C ## ZNF397、GALNT1、MAPRE2、ZNF532、KDSR、C18orf21、DTNA、RPRD1A、NARS、vps4b# # SLC39A6、RNF138、ELP2、SERPINB8、FECH、TPGS2、TRAPPC8、DSEL、KIAA1328、ST8SIA3 ##阴性:RIOK3, C18orf8, NPC1, C18orf32, RPL17-C18orf32, DYM, RPL17, CTIF, ACAA2, ttc39c# # SMAD2, MBD1, CXXC1, IER3IP1, CABYR, RBFA, ME2, HDHD2, TXNL4A, ELAC1 ## ATP9B, PIAS2, OSBPL1A, MBP, SMAD4, TSHZ1, C18orf25, CNDP1, DCC, IMPACT

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:POLD1, NAPSB, JOSD2, NR1H2, ASPDH, C19orf48, VRK3, KLK6, TBC1D17, NUP62 ## PNKP, PTOV1, ETFB, FUZ, SIGLEC10, AP2A1, SIGLEC8, CPT1C, FPR1, PRMT1 ## IRF3, ZNF577, NOSIP, ZNF649, FCGRT, ZNF350, RPS11, ZNF614, RPL13A, PPP2R1A ##ZNF506, ZNF253, ZNF14, ATP13A1, ZNF93, LPAR2, ZNF682, YJEFN3, ZNF737, NDUFA13 ## MAU2, ZNF626, SUGP1, NCAN, ZNF85, NR2C2AP, ZNF430, RFXANK, ZNF714, MEF2BNB ## ZNF431, TMEM161A, ZNF708, SLC25A42, ZNF738, ARMC6, ZNF493, SUGP2, ZNF429, HOMER3 ## pc_2 ## #阳性:NCAN, NR2C2AP, SUGP1, RFXANK, MAU2, MEF2BNB, NDUFA13, TMEM161A, YJEFN3, SLC25A42 ## LPAR2, ARMC6, ATP13A1, SUGP2, ZNF14, HOMER3, ZNF506, DDX49, ZNF253, COPE ## ZNF93, CRTC1, ZNF682, TMEM59L, ZNF737, C19orf60, ZNF626, ZNF85, UBA52, ZNF430 ##ZNF586, ZNF134, ZNF211, ZNF550, ZNF773, ZNF772, ZNF17, ZNF548, TRAPPC2P1, ZNF460 ## ZNF805, ZNF71, ZFP28, ZNF471, ZNF667, ZNF583, ERCC1, BLOC1S3, TRAPPC6A, FOSB ## GEMIN7, EML2, PNMAL1, PPP5C, HIF3A, CALM3, QPCTL, DMPK, SYMPK, ZNF542 ## PC_ 3 #阳性:UBL5, PIN1, FBXL12, ZNF812, OLFM2, ZNF562, ZNF561, C19orf66, ZNF121, PPAN ## ZNF426, EIF3G, ZNF266, ZNF177, DNMT1, FDX1L, RAVER1 ## TYK2, CDC37, KEAP1, LSM7, GADD45B, LMNB2, SPPL2B, OAZ1, TIMM13 ##阴性:RPSAP58, ZNF675, ZNF91, ZNF724P, ZNF676, ZNF43, ZNF181, ZNF100, GRAMD1A, ZNF429 ## FXYD7, ZNF493, FXYD5, USF2, ZNF738, MAG, ZNF708, TMEM147, ZNF431, RBM42 ## COX6B1, ZNF714, IGFLR1, ZNF430, U2AF1L4, ZNF85, PSENEN, ARHGAP33, ZNF626, APLP1 ## PC_ 4 ##阳性:MRPL4, S1PR2, ICAM1, DNMT1, EIF3G, FDX1L, PPAN, RAVER1, C19orf66, TYK2 ## OLFM2, CDC37, PIN1, KEAP1, UBL5, FBXL12, ZNF812, ZNF562, ZNF561, ZNF121 ## ZNF426, ZNF266, ZNF177, NFKBID, HCST, TYROBP, APLP1, SDHAF1, ARHGAP33, ALKBH6 ##阳性:AP3D1, MOB3A, PLEKHJ1, BTBD2, SCAMP4, SF3A2, UQCR11, OAZ1, MBD3, LSM7 ## C19orf25, SPPL2B, TIMM13, APC2, LMNB2, GADD45B, GNG7, SLC39A3, SGTA, ZNF580 ## ZNF581, ZNF542, ISOC2, ZNF583, SHISA7, rnf28, ZNF667, HSPBP1, ZNF583, SHISA7, rnf471, ZNF667, HSPBP1, ZNF471, SNRPD2, EML2, FOSB, APOC2, APOC1 ## QPCTL, APOE, DMPK, TOMM40, SYMPK, PVR, ZNF225, ZNF221, ZNF404, CALM3, LYPD5, SMG9, PLAUR, ZNF428 ## #阴性:Znf773, znf772, znf17, znf550, znf548, znf134, trappc2p1, znf211, znf460, znf586 ## znf805, znf71, zfp28, znf471, znf667, tyk2, raver1, cdc37, keap1, znf583 ## fdx1l, znf542, icam1, znf581, mrpl4, s1pr2, znf580, dnmt1, isoc2, eif3g

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## pc_1 ##阳性:SRSF6, L3MBTL1, CHD6, IFT52, TTPAL, ZHX3, SERINC3, PLCG1, PKIG, TOP1 ## ADA, MAFB, DHX35, YWHAB, ACTR5, TOMM34, SNHG11, STK4, KIAA1755, SYS1 ## RPRD1B, DBNDD2, TTI1, PIGT, CTNNBL1, DNTTIP1, BLCAP, SNX21, SRC, ACOT8 ##阴性:NPEPL1, STX16, VAPB, MTRNR2L3, RAE1, C20orf112, BMP7, COMMD7, MAPRE1, RTFDC1 ## CDK5RAP1, CSTF1, CBFA2T2, DOK5, NECAB3, PFDN4, PXMP4, BCAS1, RALY, ZFP64 ## EIF2S2, ATP9A, AHCY, MOCS3, ITCH, DPM1, DYNLRB1, ADNP, MAP1LC3A, PTPN1 ## pc2 ##阳性:EDEM2, EIF6, TRPC4AP, GSS, CEP250, ACSS2, ERGIC3, GGT7, TP53INP2, CPNE1 ## NCOA6, RBM12, PIGU, NFS1, MAP1LC3A, ROMO1, DYNLRB1, RBM39, ITCH, PHF20 ## AHCY, SCAND1, EIF2S2, RALY, LINC00657, PXMP4, EPB41L1, NECAB3, AAR2, LINC00657, PXMP4, EPB41L1, ZFAS1, ZNFX1, UBE2V1, DDX27, TMEM189, STAU1, PTPN1, CSE1L ## ADNP, DPM1, ARFGEF2, MOCS3, PREX1, ATP9A, ZMYND8, DOK5, TP53RK, CSTF1, ZNF334, RTFDC1, BMP7, ELMO2, RAE1 ## pc_3 ##阳性:NPEPL1, STX16, VAPB, MTRNR2L3, RAE1, C20orf112, BMP7, COMMD7, MAPRE1, RTFDC1 ## CDK5RAP1, CSTF1, CBFA2T2, DOK5, NECAB3, PFDN4, PXMP4, RALY, BCAS1, EIF2S2 ## ZFP64, AHCY, ATP9A, ITCH, MOCS3, DYNLRB1, DPM1, MAP1LC3A, ADNP, PIGU ##阴性:L3MBTL1, IFT52, SRSF6, TTPAL, CHD6, SERINC3, ZHX3, PKIG, PLCG1, ADA ## TOP1, YWHAB, MAFB, TOMM34, STK4, DHX35, SYS1, ACTR5, DBNDD2, SNHG11 ## PIGT, KIAA1755, DNTTIP1, rti1, ACOT8, CTNNBL1, ZSWIM1, BLCAP ## pc4 ##阳性:NPEPL1, STX16, VAPB, MTRNR2L3, RAE1, BMP7, RTFDC1, CSTF1, DOK5, PFDN4 ## RPN2, RBL1, MANBAL, SAMHD1, SOGA1, SRC, NDRG3, BLCAP, C20orf24, CTNNBL1 ## BCAS1, DLGAP4, TTI1, AAR2, RPRD1B, ZFP64, EPB41L1, KIAA1755, AAR2, CBFA2T2, NECAB3, PXMP4, RALY, EIF2S2, AHCY ## ITCH, CD40, NCOA5, ZNF335, SLC35C2, PCIF1, PLTP, ELMO2, CTSA, NEURL2 ## ZNF334, DYNLRB1, ZSWIM1, TP53RK, ACOT8, NCOA3, DNTTIP1, MAP1LC3A ## pc5 ##阳性:C20orf112, COMMD7, MAPRE1, NPEPL1, STX16, CDK5RAP1, VAPB, MTRNR2L3, CBFA2T2, RAE1 ## BMP7, NECAB3, RTFDC1, PXMP4, CSTF1, RALY, TTPAL, IFT52, SERINC3, L3MBTL1 ## PKIG, SRSF6, ADA, CHD6, DOK5, YWHAB, ZHX3, SRSF6, ADA, CHD6, DOK5, YWHAB, ZHX3, TOMM34, CSE1L, SLC9A8, ARFGEF2, RNF114, RBM12, CPNE1 ## NFS1, PREX1, ERGIC3, ROMO1, CEP250, RBM39, UBE2V1, EIF6, sul2, PHF20 ## EDEM2, scan1, TMEM189, LINC00657, GSS, ZMYND8, PTPN1, EPB41L1

##计算最近邻图

计算SNN

##定心缩放数据矩阵

##警告:请求的数量大于可用项目的数量(38)。##设置为38。##警告:请求的数量大于可用项目的数量(38)。##设置为38。##警告:请求的数量大于可用项目的数量(38)。##设置为38。##警告:请求的数量大于可用项目的数量(38)。##设置为38。##警告:请求的数量大于可用项目的数量(38)。##设置为38。

## pc_1 ##阳性:CCT8, USP16, BACH1, RWDD2B, TIAM1, LTN1, SOD1, N6AMT1, SCAF4, ADAMTS1 ## MIS18A, APP, URB1, GABPA, C21orf119, ATP5J, C21orf59, JAM2, SYNJ1 ##阴性:IFNGR2, IFNAR1, TEKT4P2, IL10RB, HSPA13, IFNAR2, SAMSN1, LINC00478, OLIG1, C21orf37 ## OLIG2, CXADR, BTG3, C21orf62, LINC00320, PAXBP1, NCAM2, PAXBP1- as1, MRPL39 ## pc2 ##阳性:IFNGR2, IFNAR1, IL10RB, IFNAR2, OLIG1, OLIG2, C21orf62, PAXBP1, PAXBP1- as1, SYNJ1 ## C21orf59, C21orf119, URB1, MIS18A, SCAF4, SOD1, TIAM1, BACH1, CCT8 ##阴性:TEKT4P2, HSPA13, SAMSN1, LINC00478, C21orf37, CXADR, b21orf37, ATP5J, GABPA, APP, ADAMTS1, N6AMT1, LTN1, RWDD2B, USP16 ## pc_3 ##阳性:USP16, CCT8, RWDD2B, BACH1, LTN1, TIAM1, SOD1, N6AMT1, SCAF4, ADAMTS1 ## MIS18A, APP, URB1, GABPA, C21orf59, JAM2, MRPL39 ## #阴性:TEKT4P2, IFNGR2, HSPA13, IFNAR1, SAMSN1, IL10RB, LINC00478, IFNAR2, C21orf37, OLIG1 ## CXADR, OLIG2, BTG3, BTG3, C21orf62, LINC00320, PAXBP1, NCAM2, PAXBP1- as1, SYNJ1 ## pc4 ##阳性:IFNGR2, GABPA, ATP5J, APP, IFNAR1, JAM2, ADAMTS1, N6AMT1, MRPL39, IL10RB ## NCAM2, LTN1, IFNAR2, LINC00320, RWDD2B, OLIG1, BTG3, USP16, OLIG2 ##阴性:TEKT4P2, URB1, C21orf119, MIS18A, HSPA13, SCAF4, C21orf59, SOD1, SAMSN1, SYNJ1, LINC00478, BACH1, PAXBP1, C21orf37, CCT8, C21orf59, CXADR ## pc5 #阳性:MRPL39, NCAM2, SYNJ1, C21orf59, JAM2, PAXBP1- as1, LINC00320, PAXBP1, C21orf119, atp5j# # C21orf62, BTG3, URB1, GABPA, OLIG2, CXADR, MIS18A, APP, OLIG1 ##阴性:USP16, IFNGR2, CCT8, RWDD2B, TEKT4P2, BACH1, HSPA13, IFNAR1, LTN1, SOD1, LINC00478, IFNAR2, ADAMTS1, SCAF4, C21orf37

##计算最近邻图

计算SNN

##定心缩放数据矩阵

## PC_ 1 ##阳性:RABL2B, CHKB, CPT1B, SCO2, NCAPH2, LMF2, PPP6R2, DENND6B, PLXNB2, MAPK12 ## TUBGCP6, TRABD, GSTT2B, MLC1, DDT, CRELD2, GSTT2, ALG12, GSTT1, FAM19A5 ## CABIN1, TBC1D22A, SPECC1L, guucd1, SNRPD3, FAM211B, SGSM1, CRYBB2P1, TTLL12, SEZ6L ##阴性:CYTH4, MFNG, MPST, CDC42EP1, TST, GGA1, NCF4, PDXP, IFT27, LGALS1 ## EIF3D, FOXRED2, TXN2, MYH9, APOL2, H1F0, GCAT, APOL4, ANKRD54, RBFOX2 ## EIF3L, MCM5, POLR2F, HMOX1, PLA2G6, TOM1, MAFF, HMGXB4, TMEM184B, CSNK1E ## pc2 ##阳性:ZMAT5, NF2, UQCR10, NIPSNAP1, THOC5, ASCC2, AP1B1, MTMR3, RASL10A, osm# # EWSR1, GATSL3, TBC1D10A, RHBDD3, SF3A1, ZNRF3-AS1, SEC14L2, MTFP1, XBP1, GAL3ST1 ## PES1, CCDC117, OSBP2, MORC2-AS1, HSCB, TUG1, TTC28, SELM, TTC28- as1, RNF185 ##阳性:PMM1, POLR3H, ACO2, PHF5A, DESI1, TOB2, XRCC6, TEF, NHP2L1, SREBF2 ## ZC3H7B, NDUFA6, CHADL, L3MBTL2, RRP7A, EP300, RRP7B, RBX1 ## POLDIP3, XPNPEP3, CYB5R3, ST13, ARFGAP3, SLC25A17, PACSIN2, MKL1, TTLL1, TUBGCP6, PPP6R2, TRABD, LMF2, NCAPH2, MLC1, SCO2 ## CRELD2, CPT1B, CHKB, ALG12, RABL2B, FAM19A5, TBC1D22A, TTLL12, TSPO, MCAT ## TTLL1, PACSIN2, FAM211B, SGSM1, SNRPD3, CRYBB2P1, GUCD1, SPECC1L, ARFGAP3, SEZ6L ##LGALS1, PDXP, GGA1, CDC42EP1, H1F0, MFNG, CYTH4, GCAT, MPST, ANKRD54 ## EIF3L, TST, POLR2F, NCF4, PLA2G6, IFT27, MAFF, TMEM184B, EIF3D, CSNK1E ## FOXRED2, DDX17, TXN2, CBY1, MYH9, TOMM22, APOL2, jot1b, SCO2, NCAPH2, LMF2, PPP6R2, DENND6B, PLXNB2, MAPK12 ## TUBGCP6, TRABD, MLC1, CRELD2, ALG12, FAM19A5, TBC1D22A, SYN3, FBXO7, TIMP3 ## YWHAH, HMGXB4, MCM5, PISD, RBFOX2, EIF4ENIF1 ##GSTT2B, DDT, GSTT2, GSTT1, CABIN1, SPECC1L, GUCD1, SNRPD3, FAM211B, sgsm4, TFIP11, MIAT, PITPNB, TTC28- as1, TTC28, HSCB, CCDC117 ## ADSL, SGSM3, TNRC6B, MKL1, RPS19BP1, ATF4, SLC25A17, TAB1, ST13, SYNGR1 ## pc5 ##阳性:ACO2, POLR3H, PHF5A, PMM1, TOB2, DESI1, TEF, XRCC6, PES1, zc3h7bgal3st1, OSBP2, MORC2-AS1, NHP2L1, MTFP1, RANGAP1, TUG1, SEC14L2, SREBF2, SF3A1 ## SELM, CHADL, TBC1D10A, RNF185, GATSL3, NDUFA6, L3MBTL2, OSM, PIK3IP1 ##阴性:Gstt2b, rabl2b, ddt, chkb, gstt2, cpt1b, gstt1, sco2, ncaph2, cabin1 ## lmf2, specc1l, ppp6r2, dennd6b, gucd1, plxnb2, lgals1, pdxp, h1f0, gga1 ## mapk12, gcat, ankrd54, snrpd3, cdc42ep1, eif3l, mfng, polr2f, tubgcp6, cyth4

##计算最近邻图

计算SNN

运行inferCNV的基本输出。

3．1在线文档

有关文件、用法和教程的其他说明，请访问维基。

3.2TrinityCTAT

该工具是TrinityCTAT工具包的一部分，专注于利用RNA-Seq来更好地了解癌症转录组。欲了解更多，请访问TrinityCTAT

3．3应用程序

该方法被用于:

Anoop P. Patel等人。单细胞RNA-seq在原发性胶质母细胞瘤中显示瘤内异质性。科学，2014年6月20日:1396-1401

通过单细胞RNA-seq分析转移性黑色素瘤的多细胞生态系统。《科学》2016年4月8日;352(6282):189-96