Unsupervised machine learning methods for classifying a lupus disease state of a subject

A method for classifying and treating a type 1 lupus disease state or type 2 lupus disease state of a subject, the method comprising:

• (a) obtaining a subject data set comprising or derived from gene expression measurements data of at least 21 genes from a biological sample obtained or derived from the subject, wherein the at least 21 genes are each selected from at least 21 different gene sets, and wherein the different genes sets are selected from:
• a first gene set comprising:
• DDX11L9, MT-ATP6, DDX11L1, MT-ND4, MT-ND2, MT-ND4L, DDX11L2, MT-ATP8, MT-CO3, MT-CYB, MT-ND5, MT-CO2, DDX11L16, MT-ND3, DDX11L17, MT-ND1, DDX11L5, FN1, CFAP45, MT-ND6, LMNA, VIPR2, MIR23AHG, DDX11L10, IQCN, TUBB6, SPOCD1, SLC22A23, APOA1-AS, HSD17B7P2, ZSWIM4, PKNOX2, BLM, SCN5A, MTMR9LP, SNPH, MT-TE, MEX3B, LINC00658, OR7E94P, MT-CO1, DDX11L8, SLC39A4, DGKH, LINC02745, MIR23A, NPAPIL, GHRLOS, FBXO5, NETO2, ATP1B1, BNIP3P1, RTN4RL1, PELATON, ELF3, NOL3, and CHD1L;
• a second gene set comprising:
• MT-ATP6, MT-ND4, MT-ND2, MT-ND4L, MT-ATP8, MT-CO3, MT-CYB, MT-ND5, MT-CO2, MT-ND3, MT-ND1, FN1, MT-ND6, VIPR2, SPOCD1, SLC22A23, APOA1-AS, HSD17B7P2, BLM, MTMR9LP, SNPH, MT-TE, MEX3B, MT-CO1, SLC39A4, DGKH, LINC02745, NPAPIL, NETO2, BNIP3P1, RTN4RL1, and PELATON;
• a third gene set comprising:
• MT-ATP6, MT-ND4, MT-ND2, MT-ND4L, MT-ATP8, MT-CO3, MT-CYB, MT-ND5, MT-CO2, MT-ND3, MT-ND1, MT-ND6, VIPR2, SPOCD1, BLM, MTMR9LP, SNPH, MT-TE, MT-CO1, SLC39A4, DGKH, RTN4RL1, and PELATON;
• a fourth gene set comprising:
• BMS1P15, SSH2, HCG27, LGALS9B, ADAMTSL4-AS2, ADAMTSL4-AS1, NEDD9, FAR2, ZNF615, DNAH17, BTN1A1, TUBA1C, BMS1P16, BMS1P11, GLI1, BMS1P9, FAAHP1, OR52B3P, VNN1, L0INC02656, SLC31A2, LINC01093, CNRIP1, ZDHHC19, IFITM3P2, TMEM119, MIR24-2, SEMA3B, ZNF718, BEAN1, TRAV13-2, ALDH1A2, PROKR2, RBM47, BNIPL, CSF1, AVP, SALL2, FRGCA, MRPL19, EPHB1, NEFL, LGALS9C, CDRT15, IL6R-AS1, CAPN13, TMEM221, KRT7, ENAH, PCP4L1, MCPH1-AS1, OR11H2, CD164L2, SMPDL3B, LINC02421, KIF27, BSPRY, PTOV1-AS1, TEK, SPACA6, IGHD3-10, KLK1, TRAV20, KCTD15, CELSR3, CCL4L2, LINC01791, MY06, KRT74, CLEC40, TPTEP2, CALML6, PRSS16, IDI2-AS1, PPM1F-AS1, BTNL3, PMFBP1, GGTLC2, CASC2, GRM2, BMS1P10, LINC01882, PLXNA4, MIR3648-2, EFR3B, WNT1, PICK1, MDM2, NUPR1, CNIH2, KCNJ3, CFAP43, TULP2, SLC52A3, FGGY, RPS3AP18, FBXO24, RTEL1, ANK3-DT, CA12, OR51RIP, H4C6, TAFA1, BOK, NANOS3, ARHGAP22, NSG1, SLC25A18, and CNTF;
• a fifth gene set comprising:
• HCG27, ADAMTSL4-AS2, ADAMTSL4-AS1, FAR2, DNAH17, BTN1A1, TUBA1C, GLI1, FAAHP1, LINC02656, LINC01093, ZDHHC19, IFITM3P2, TMEM119, MIR24-2, SEMA3B, ALDH1A2, RBM47, BNIPL, CSF1, NEFL, CAPN13, TMEM221, KRT7, ENAH, PCP4L1, SMPDL3B, TEK, SPACA6, IGHD3-10, KLK1, KCTD15, LINC01791, MYO6, KRT74, PRSS16, GRM2, PLXNA4, MIR3648-2, WNT1, MDM2, CNIH2, TULP2, SLC52A3, FGGY, RPS3AP18, ANK3-DT, CA12, H4C6, TAFA1, NANOS3, ARHGAP22, and CNTF;
• a sixth gene set comprising:
• HCG27, ADAMTSL4-AS2, ADAMTSL4-AS1, FAR2, DNAH17, BTN1A1, TUBA1C, GLI1, FAAHP1, LINC02656, LINC01093, ZDHHC19, IFITM3P2, TMEM119, MIR24-2, SEMA3B, ALDH1A2, RBM47, BNIPL, CSF1, NEFL, CAPN13, TMEM221, PCP4L1, SMPDL3B, TEK, SPACA6, KLK1, KCTD15, LINC01791, MY06, KRT74, PRSS16, GRM2, PLXNA4, MIR3648-2, WNT1, MDM2, CNIH2, TULP2, SLC52A3, FGGY, RPS3AP18, ANK3-DT, CA12, TAFA1, NANOS3, ARHGAP22, and CNTF;
• a seventh gene set comprising:
• IQCD, LMX1B, ABCC11, CEACAM22P, LINC01629, LINC02288, SCN2B, NYAP1, KLRC1, GSTM2, OR7E66P, ELAPOR1, GGT8P, DNM1, PRRT1B, CDH22, COL6A5, PGC, TRBD1, F12, and PSCA;
• an eighth gene set comprising:
• C1QB, NOG, MPP2, C1QC, SLC22A17, SPEG, CNN3, C1QA, LGALS1, GOLGA6L9, TRBV28, NT5E, C14orf132, LDHD, KIR3DX1, GSTA6P, PATL2, KRT5, PPP4R1-AS1, ATP1A4, AMPD2, LINC01293, PCBP3, EVC, SOX8, RP1L1, UNC119B, MCF2L, ANXA2P2, MDS2, ATP2B2, EPS8L1, CALD1, ZNF812P, CASQ1, PARP11-AS1, TSPAN6, and E2F2;
• a ninth gene set comprising:
• NOG, SLC22A17, SPEG, CNN3, C1QA, LGALS1, GOLGA6L9, NT5E, KIR3DX1, GSTA6P, PATL2, KRT5, ATP1A4, AMPD2, EVC, SOX8, ANXA2P2, MDS2, ATP2B2, EPS8L1, CASQ1, PARP11-AS1, TSPAN6, and E2F2;
• a tenth gene set comprising:
• IFI44L, SPATS2L, RSAD2, IFI44, DDX60, EIF2AK2, USP18, DDX58, CMPK2, HERC5, IFIT5, IFIH1, IFI6, EPSTI1, MX1, PLSCR1, PNPT1, FAM247A, ISG15, ZCCHC2, IFI27, SAMD9L, SMTNL1, STAT1, CHMP5, STAT2, GBP1, HERC6, PARP9, PHF11, SIGLEC1, OAS1, USP41, LY6E, MIR4477B, SAMD9, MTCO1P53, CCDC194, FAM230D, PARP12, IFI16, RSPH9, DDX60L, TUBA8, EPB41L5, TMEM123, ACO1, CETP, GBP1P1, KRT72, HES4, ODF3B, TRIM5, TYMP, FAM230H, PARP14, HESX1, APOL6, KLHDC7B, EPHB2, LY6E-DT, LIPA, FBX039, KIAA1958, ACOT9, LAMP3, NRIR, LGALS3BP, SCO2, UNC93B3, FRG1HP, KRT73, IFITM3P4, UNC93B5, XAF1, NEXN, LINC00487, TIMM10, ZNF684, EDAR, TENT5A, TDRD7, LINC02785, LAP3, DOCK4, PLSCR2, MIR4477A, DTX3L, CCL3L1, CHRNB2, KANK3, CMTR1, TSPOAP1, GPRC5C, UTS2B, GBP4, PPMIK-DT, IL2RB, CCR5AS, NCR3, ATF3, NOS2P2, RGL1, GRAMD1B, RHAG, GPD2, FEZ1, CCRL2, UNC93B7, FAM230A, NKD1, IGHV5-10-1, OR52K2, ITGA10, LTK, PRR5L, C8orf31, CLEC2B, FAM230E, FCN1, ENTPD1-AS1, HIC1, OTOF, PTGFR, SEZ6L, OSBPL6, FLT4, GBP5, GALM, CCL2, FAM131B, DNM1P47, MS4A4A, CCR12P, ANTXRLP1, APOBEC3B-AS1, SPON1, HLA-G, CD274, FITM1, CACNA2D2, CAPN5, PITPNM3, CD300C, ADPRH, RASGRF2, TBPL2, LINC02574, TSPAN15, GDF7, LDLRAD3, LPAL2, KRT73-AS1, AXL, LRRC71, GPRC5D-AS1, HLA-F-AS1, PDCD1LG2, TRBV6-2, LINC02446, TCN2, C3AR1, ISM1, TMEM255A, SLFN5, ITGA9-AS1, LINC00638, CACNA1I, LILRB4, CD14, KIT, MYCL, SNTG2, CCL8, BLVRA, PIMREG, CACNA1A, IGHE, COL5A1, MT1DP, SLC7A8, ZNF600, CD300E, CHN1, LINC02754, SLPI, NECTIN2, PLB1, SSC4D, MTCO1P40, PLPP2, EMP1, NID1, LINC01163, GPM6A, H3C6, EBF4, ACBD7, IGHV3-64D, ERFE, LINC00243, FAM3D, SLC26A5, LRRC36, LINC02068, FBLN2, HCG9, CTSL, NOS2P3, FOLR3, RTN1, COLGALT2, TEKT1, HID1, KCNH7, PID1, TDRG1, SLC8A3, FUT2, MID2, RGPD2, NCAPG2, ULBP2, GNG5, IL15, CMKLR1, OCLNP1, GRIK4, LINC01918, RUFY4, MYOF, KCNJ2, CCL20, CRIP2, TPSD1, FAM66D, S100A7, LINC01344, HEY2, SCGB1C2, FAM178B, SCARB2, ISLR2, CYP21A1P, P3H3, KIAA1841, FAM247B, AGRN, SP100, RNF213, FAM230B, REC8, FRG1KP, ANXA10, GNB4, MILR1, KYNU, FRMD3, DNAJA1, PGAP1, SAMD4A, PRAL, CDH24, GBP3, ADAMTS10, DLG5, LMO2, SDS, UNC93B4, LHFPL2, VSIG1, FAM209A, GALNT12, PPFIBP1, LINC01484, SAMD15, MTHFD1L, PMEL, ZNF514, SLITRK5, AK5, LINC01504, EPHB3, DNAJC15, REELD1, NR3C2, NR2F1-AS1, ALS2CL, MIR503HG, IL17RE, KCNC3, MAFA, CYP46A1, RARRES2, FKBP10, FAM170B-AS1, USP13, BTN2A3P, TRAJ25, RPS2P7, JPH4, LRP12, LINC01307, PPP1R27, RNF213-AS1, CHCHD2P8, CAMK2N1, SLC7A10, GLIS3, PTRH1, Clorf127, MYG1-AS1, H4C12, HCAR1, CMTM8, TRBV7-1, ZNF835, ITGA7, CSPG4P11, MMP17, LSP1P4, CA8, EGR3, CYP4F12, DPYS, ZNF208, CPB1, SYNDIG1L, RETREG1, and MPPED1;
• an eleventh gene set comprising:
• IFI44L, SPATS2L, RSAD2, IFI44, DDX60, EIF2AK2, USP18, DDX58, CMPK2, HERC5, IFIT5, IFIH1, IFI6, EPSTI1, MX1, PLSCR1, PNPT1, FAM247A, ISG15, ZCCHC2, IFI27, SAMD9L, SMTNL1, CHMP5, STAT2, HERC6, PARP9, PHF11, SIGLEC1, OAS1, USP41, LY6E, MIR4477B, SAMD9, CCDC194, PARP12, IFI16, RSPH9, DDX60L, TUBA8, EPB41L5, TMEM123, ACO1, CETP, HES4, TRIM5, PARP14, HESX1, KLHDC7B, LIPA, KIAA1958, ACOT9, LAMP3, NRIR, LGALS3BP, FRG1HP, XAF1, LINC00487, TIMM10, ZNF684, EDAR, TDRD7, LINC02785, DOCK4, PLSCR2, MIR4477A, DTX3L, CHRNB2, KANK3, CMTR1, TSPOAP1, CCR5AS, GRAMD1B, RHAG, GPD2, FEZ1, CCRL2, NKD1, IGHV5-10-1, OR52K2, LTK, PRR5L, FAM230E, HIC1, OTOF, FAM131B, CCR12P, ANTXRLP1, APOBEC3B-AS1, SPON1, HLA-G, CACNA2D2, RASGRF2, LINC02574, TSPAN15, GDF7, LPAL2, AXL, HLA-F-AS1, ITGA9-AS1, LINC00638, CACNA1I, CCL8, PIMREG, COL5A1, MT1DP, ZNF600, EMP1, GPM6A, EBF4, IGHV3-64D, LINC00243, SLC26A5, LINC02068, HCG9, SLC8A3, RUFY4, S100A7, HEY2, SCARB2, CYP21A1P, P3H3, KIAA1841, FAM247B, AGRN, SP100, RNF213, REC8, FRG1KP, ANXA10, GNB4, MILR1, FRMD3, DNAJA1, PGAP1, SAMD4A, PRAL, DLG5, UNC93B4, LHFPL2, VSIG1, PMEL, SLITRK5, NR3C2, ALS2CL, IL17RE, FKBP10, USP13, BTN2A3P, TRAJ25, RPS2P7, JPH4, PPP1R27, RNF213-AS1, CAMK2N1, Clorf127, ZNF835, CSPG4P11, CA8, and SYNDIG1L;
• a twelfth gene set comprising:
• IFI44L, RSAD2, IFI44, DDX60, EIF2AK2, DDX58, CMPK2, HERC5, IFIT5, IFIH1, IFI6, EPST1, MX1, PLSCR1, PNPT1, ISG15, ZCCHC2, IFI27, SAMD9L, SMTNL1, CHMP5, PARP9, PHF11, SIGLEC1, MIR4477B, SAMD9, CCDC194, IFI16, RSPH9, DDX60L, EPB41L5, TMEM123, ACO1, PARP14, HESX1, LIPA, KIAA1958, ACOT9, NRIR, XAF1, LINC00487, TIMM10, ZNF684, TDRD7, LINC02785, DOCK4, PLSCR2, MIR4477A, DTX3L, CHRNB2, KANK3, TSPOAP1, CCR5AS, RHAG, GPD2, CCRL2, NKD1, IGHV5-10-1, OR52K2, LTK, PRR5L, HIC1, FAM131B, ANTXRLP1, APOBEC3B-AS1, LINC02574, TSPAN15, LPAL2, AXL, HLA-F-AS1, CACNA1I, PIMREG, COL5A1, ZNF600, EBF4, LINC00243, LINC02068, HCG9, S100A7, HEY2, SCARB2, CYP21A1P, KIAA1841, AGRN, SP100, FRG1KP, ANXA10, GNB4, MILR1, FRMD3, DNAJA1, PGAP1, PRAL, DLG5, UNC93B4, LHFPL2, VSIG1, PMEL, FKBP10, BTN2A3P, TRAJ25, RPS2P7, CAMK2N1, CSPG4P11, and SYNDIG1L;
• a thirteenth gene set comprising:
• SPATS2L, USP18, FAM247A, STAT2, HERC6, OAS1, USP41, LY6E, PARP12, TUBA8, CETP, HES4, TRIM5, LAMP3, LGALS3BP, CMTR1, GRAMD1B, FAM230E, CCL8, GPM6A, P3H3, FAM247B, RNF213, REC8, SAMD4A, JPH4, and RNF213-AS1;
• a fourteenth gene set comprising:
• KRT72, EPHB2, KRT73, LAP3, MS4A4A, LDLRAD3, KRT73-AS1, TCN2, C3AR1, LILRB4, BLVRA, CD300E, SSC4D, NID1, FBLN2, CTSL, HID1, MYOF, AK5, LINC01504, MIR503HG, CYP46A1, RARRES2, FAM170B-AS1, and LINC01307;
• a fifteenth gene set comprising:
• ODF3B, TYMP, LY6E-DT, FBX039, SCO2, UNC93B3, IFITM3P4, UNC93B5, PPMIK-DT, UNC93B7, ITGA10, ENTPD1-AS1, OSBPL6, FLT4, FITM1, CAPN5, LRRC71, TRBV6-2, LINC02446, ISM1, KIT, CACNA1A, IGHE, SLC7A8, CHN1, LINC02754, SLPI, ACBD7, ERFE, LRRC36, FOLR3, TEKT1, FUT2, MID2, RGPD2, ULBP2, IL15, LINC01918, LINC01344, FAM178B, ISLR2, ADAMTS10, GALNT12, PPFIBP1, MTHFD1L, ZNF514, EPHB3, DNAJC15, MAFA, LRP12, TRBV7-1, ITGA7, LSP1P4, and RETREG1;
• a sixteenth gene set comprising:
• SRGAP2B, FAM225A, CSAG3, SRGAP2C, SRGAP2, RNF175, FCER1A, RNASE2, ANKRD35, WNT7A, FAM225B, ROBO3, TLR2, ZFP57, RETN, PTGDR2, LINC02458, SLC12A1, ZNF595, TARM1, KRT8P26, DBH, DISC1, TAF11L2, MAOA, TLE2, UPB1, IL4, CC2D2A, OLFML2A, KCNG1, C1QTNF7-AS1, MYOM2, DEPDC1, LINC01238, LINC02761, DBNDD1, UCKL1-AS1, LINC00884, LGALSL-DT, DPYSL4, SLC45A3, SLC4A3, ACTBP8, LMO7, CNR1, SRGAP2D, CCDC162P, C3orf20, LINC02568, WARS1, ESPNP, H2AC13, LINC02520, TRAJ20, TRAV14DV4, SEPTIN9-DT, GRB10, NPTXR, GSDMC, ZNF727, SLC16A11, ASPH, MTIE, CPA5, C1QTNF7, CCDC144B, CDK2AP2P2, C5orf64, CSAG2, ACSM3, MOG, OR52B4, FMNL2, EXT1, MROCK1, LINC02042, PLEKHB1, NPM2, LINC00398, SPTBN5, CYP1A1, LINC02287, BRD7P5, SPC24, EFNA3, PNMT, FOXRED2, PODXL2, TRAJ32, LHFPL3-AS2, and MIR150;
• a seventeenth gene set comprising:
• SRGAP2B, FAM225A, SRGAP2C, SRGAP2, RNASE2, ANKRD35, WNT7A, FAM225B, ROBO3, RETN, ZNF595, TARM1, DBH, TAF11L2, TLE2, DEPDC1, LINC01238, UCKL1-AS1, SLC45A3, LM07, ESPNP, TRAJ20, NPTXR, GSDMC, SLC16A11, ACSM3, FMNL2, PLEKHB1, LINC02287, PNMT, FOXRED2, and TRAJ32;
• an eighteenth gene set comprising:
• CSAG3, RNF175, FCER1A, TLR2, PTGDR2, LINC02458, SLC12A1, DISC1, MAOA, UPB1, CC2D2A, OLFML2A, C1QTNF7-AS1, LGALSL-DT, SLC4A3, SRGAP2D, CCDC162P, LINC02568, WARS1, SEPTIN9-DT, GRB10, ZNF727, ASPH, C1QTNF7, CSAG2, OR52B4, EXT1, MROCK1, LINC02042, LINC00398, CYP1A1, PODXL2, and LHFPL3-AS2;
• a nineteenth gene set comprising:
• KRT17P2, KRT17P1, CPT1A, ADGRE4P, PRSS33, SIGLEC8, ALOX15, NME4, HRH4, CACNG6, SLC45A2, FAM138B, COL26A1, CACNG8, IL5RA, CLC, DNASE1L3, PTMS, WARS1P1, RHOXF1P1, COL11A2, SLC4A9, COLEC12, KRT17P6, PDK4, SMPD3, IL34, CNTN4-AS1, LINC01226, SLC25A20, ADAMTS7P1, ARHGEF35-AS1, SPNS3, EPHA2, ANOS1, ENPP7P8, RPL35AP26, SLC29A1, KRT2, TFEC, LINC01300, HPN, and PTPRF;
• a twentieth gene set comprising:
• ADGRE4P, PRSS33, SIGLEC8, ALOX15, HRH4, CACNG6, COL26A1, CACNG8, IL5RA, CLC, DNASE1L3, PTMS, RHOXF1P1, COL11A2, SLC4A9, SMPD3, IL34, LINC01226, ADAMTS7P1, SPNS3, EPHA2, ENPP7P8, RPL35AP26, SLC29A1, and TFEC;
• a twenty-first gene set comprising:
• EPN2, MKI67, CCNA2, TPX2, BUB1, BIRC5, TOP2A, GTSE1, CDC20, CIT, PKMYT1, ESPL1, KCNH3, ASPM, ADAM23, HJURP, KIF18B, KIFC1, TROAP, NCAPG, MIXL1, CDK1, CDC25A, CDC45, CDKN3, ZC2HC1C, INAVA, OR13A1, HMGB3, IGHV1-3, NUF2, KIF4A, POLR2J3, DLGAP5, STIL, CBLN2, MCM10, RNA5SP315, HMMR, GRAPL, NCAPH, CDT1, ATP5MGP1, CPAMD8, RFPL4A, ICA1, COPS5P2, LINC00683, CNGB1, TWIST2, FIGNL2, CIDP5, CDCA3, PACSIN1, MTND4P24, KLHL33, FPGT-TNNI3K, CCNB2, KIF11, INSL6, NDC80, VPS33B-DT, LINC00475, DNM1P31, TSPAN3, HTR1E, SLC7A11, SLC9C1, CD38, GSDME, SKA1, HAUS6P1, TEDDM1, MYRFL, MTCL1, WBP1LP2, BMP8B, PDGFC, SNHG5, and LINC02610;
• a twenty-second gene set comprising:
• MKI67, CCNA2, TPX2, BUB1, TOP2A, GTSE1, CDC20, CIT, HJURP, KIF18B, KIFC1, NCAPG, MIXL1, CDK1, CDC45, CDKN3, NUF2, MCM10, CDT1, CNGB1, TWIST2, FIGNL2, CDCA3, PACSIN1, MTND4P24, CCNB2, INSL6, TSPAN3, CD38, SKA1, TEDDM1, and MYRFL;
• a twenty-third gene set comprising:
• HBB, FAM210B, ADIPOR1, PBX1, EMC3, FBX07, PPMIA, PAGE2B, LINC01036, SLC25A37, PAGE2, RGS10, SLC6A19, KCNMA1, TPGS2, BBOF1, FUNDC2P1, Clorf198, BEND3P1, and LEFTY1;
• a twenty-fourth gene set comprising:
• TUFT1, KIAA0319, ABCA1, CORIN, ABCG1, VASH1, NFXL1, STARD10, NMRAL2P, RPA2, COL9A3, LINC00222, LINC01305, LINC01644, TMEM273, SYT17, SLC3A2, NEO1, PTPN5, and DNM1P34;
• a twenty-fifth gene set comprising:
• SC5D, KBTBD8, PRELID3B, CCDC82, C12orf29, PRKAR2A-AS1, UGT8, IGIP, SRP9, RLN2, CFAP54, UFL1, LRRC3, NAP1L3, NCAM2, UTP15, RLN1, CFAP100, CENPE, ZNF404, PTPN13, SMIM10L2A, CD207, LRFN2, ANKRD12, KLRA1P, LINC00698, TMEM158, LVRN, ZNF471, LINC02575, ZNF204P, RIN1, CHEK2P2, HLTF, ALKAL2, MYCT1, SPAG8, EXD2, LINC00402, XIRP1, GK4P, CPNE4, ITPR1-DT, and UNC5A;
• a twenty-sixth gene set comprising:
• SC5D, KBTBD8, PRELID3B, C12orf29, UGT8, IGIP, RLN2, CFAP54, UFL1, LRRC3, NAP1L3, UTP15, ZNF404, PTPN13, SMIM10L2A, CD207, ANKRD12, LINC00698, LVRN, ZNF471, LINC02575, HLTF, MYCT1, SPAG8, EXD2, LINC00402, XIRP1, CPNE4, and ITPR1-DT;
• a twenty-seventh gene set comprising:
• SC5D, KBTBD8, PRELID3B, C12orf29, UGT8, IGIP, RLN2, UFL1, LRRC3, NAP1L3, UTP15, ZNF404, PTPN13, SMIM10L2A, ANKRD12, LINC00698, LVRN, LINC02575, HLTF, MYCT1, SPAG8, EXD2, XIRP1, CPNE4, and ITPR1-DT;
• a twenty-eighth gene set comprising:
• RASIP1, IL9RP1, SEC61G-DT, MAP1B, PLIN1, ZNF436-AS1, KRT18, OLFM1, SEMA3F, IRAG1-AS1, CALCB, GRM7, HOXC4, FGF17, ARHGAP5-AS1, LINC02280, LINC02666, RN7SKP1, ZNF165, CFAP299, LINC02356, and DNM1P33;
• a twenty-nineth gene set comprising:
• RPS26P6, RPS26P8, RPS26P58, ANK2, RPS26, RPS26P13, CHST6, LINC02175, EBF3, RPS26P2, OR52P2P, PERM1, RGMA, CFAP46, CREB3L3, RPS26P39, DAB1, TINCR, ZMYND15, and LINC02141;
• and
• a thirtieth gene set comprising:
• RPS26P6, RPS26P8, RPS26P58, ANK2, RPS26, RPS26P13, CHST6, LINC02175, EBF3, RPS26P2, OR52P2P, PERM1, CFAP46, CREB3L3, RPS26P39, DAB1, TINCR, ZMYND15, and LINC02141;
• (b) classifying the subject as having the type 1 lupus disease state or the type 2 lupus disease state of the subject using a machine-learning model to process gene expression levels of at least a subset of the at least 21 gene sets in the gene expression measurements data;
• and
• (c) administering a treatment to the subject, wherein the treatment comprises Prednisone, Hydroxychloroquine, Methotrexate (MTX), Cyclophosphamide (CTX), Mycophenolate mofetil (MMF), Azathioprine (AZA), Belimumab, Anifrolumab, or Voclosporin when the subject is classified as having the type 1 lupus disease state, or wherein the treatment comprises Duloxetine, Gabapentin, Milnacipran, or Pregabalin when the subject is classified as having the type 2 lupus disease state.