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. Author manuscript; available in PMC: 2013 Jun 4.
Published in final edited form as: Cytogenet Genome Res. 2013 Apr 3;139(3):206–214. doi: 10.1159/000348433

Table 1.

Composition of the clades of interest from the cladogram of figure 1 and their synapomorphies

Clade 1
19 Specimens: all from HNTDI
GSM512558, GSM512561, GSM512562, GSM512564, GSM512565, GSM512566, GSM512567, GSM512568, GSM512569, GSM512570, GSM512571, GSM512572, GSM512574, GSM512575, GSM512576, GSM512577, GSM512578, GSM512579, GSM512580
45 Synapomorphies
ATP5E, ATP5SL, BLCAP, C19orf10, CALD1, CAPN7, FAM65A, FLOT1, FNDC3B, GANAB, H2AFX, HNRNPA1, HSPD1, IFI35, JUN, KIAA1033, LARP4B, LONP2, LPAL2, MKNK1, MSH6, MYCBP2, NGLY1, ORC2L, PLSCR3, PPCDC, PRDX2, PSMB2, R02172, RAB7A, RARS, RBM16, RBX1, RPIA, SLC25A14, SLC35D2, SNRPB, SWAP70, TARDBP, TEAD4, TIMP1, TRADD, TUBA1C, UBXN7, UQCRC2
  Subclade 1a, 43 synapomorphies
  AKR1C3, ANXA4, ARPC3, BBS9, BLZF1, C3, CTSB, DDR2, EIF3G, ESPL1, FRMD1, GM2A, GPX1, GPX7, HLA-DQA1, IER3, IGF1, LARS2, LGALS3BP, LPAR1, LPCAT1, MED28, MIR936, MSLN, MXRA8, NF1, NLRP1, NPM3, NR4A2, NUDT1, PLTP, PSKH1, QPRT, RPL10P10, RPL28, RPRM, SERTAD2, SRSF1, SSR4, TFAP2A, YTHDF1, ZFP64, ZNF451
  Subclades 1b–e, 49 synapom orphies
  ADAM8, AP2A2, ATP5C1, ATP5C1, AU146983, BAZ1B, BCL7B, CAPZB, CBX6, COMMD4, CSNK1D, CSTB, DDX3X, DNMT1, DUSP8, EDNRB, EPHB4, FRAT2, FYCO1, KLF11, KPNB1, LPPR2, LSM6, MAGEF1, MED27, MRPS31, MTIF2, NAA35, NAP1L1, P4HB, PBXIP1, PDLIM4, PLA2G4B, RAB3GAP1, RARA, RCN3, RNF13, SERINC3, SNRK, SNRNP200, SON, SPTLC2, TMCO6, TMEM159, TMEM2, TMSL3, TNS4, UBR5, ZMYM4
  Subclades 1c–e, 110 synapomorphies
  SEPTIN5, AA719797, ACTB, ADD1, AL109716, ALG6, AMACR, ARFGEF1, ARHGAP11A, ARHGEF7, ARL4A, ARL6IP5, ARNT, ASH1L, ATP6V1B2, BAALC, BAT2, BBS9, BST2, C11orf21, C1orf144, CACNA1A, CBWD7, CD84, CDV3, COL16A1, COMMD3, CSNK1G2, CXCL9, DAZAP1, DECR1, DFNB31, EFNA2, EIF3G, ERP44, F12, FAM125B, FLJ11292, FSHB, FTL, GMEB2, GNAI2, GOLGA1, H49077, HAO1, HIRA, HNRNPL, HNRNPM, ILF3, ITFG1, JMJD6, KCNMB4, KDM5B, KIAA1009, KLHL2, KLRG1, LOC100132247, LOC441899, MACROD1, MAT2A, MON1B, MRAS, MRPL39, MYST2, NDUFS4, NGRN, NLRP1, NSA2, NXT1, PIGC, PPP2R3A, PPP4C, PRDM2, PRUNE, PSMF1, RAD1, RAD23A, RGS5, RHOD, RIOK3, RNF25, RPL28, RPL3, RPLP0, RPLP1, RPP30, RPS16, RPS2, RPS21, RPS3A, RUSC1, SFI1, SFT2D2, SIGLEC6, SIPA1L1, SLC11A2, SNURF, SPTBN1, SRI, STX6, TAF1, THBS1, TRIM32, TRPC1, UBE2Q1, UNC50, WDR1, WDR55, ZNF287, ZNF350

Clade 2
14 Specimens: all from HNTDI
GSM242014, GSM242015, GSM242017, GSM242018, GSM242022, GSM242023, GSM242024, GSM242025, GSM242026, GSM242027, GSM512557, GSM512559, GSM512563, GSM512573
5 Synapomorphies:
CYR61, DUSP1↓, EIF1↓, FOSB, TACSTD2
  Subclade 2a, 54 synapomorphies
  AHNAK, AK000834, AK025360, AKAP13, AL109696, ANKFY1, AP1M2, ARID3B, C1orf116, CCDC88C, CHRNA1, CLCN6, COL4A3, CROCC, DUSP12, DZIP3, EPS8L1, ERLIN2, ERO1LB, FER, FOXO4, GATC, GUSBP3, HOXA5, LHB, MAGEA3, MCOLN1, MXD4, MZF1, PAIP2B, PLGLB1, PRPF39, PRSS22, RB1CC1, RERGL, ROR2, SKAP2, SLC33A1, SLC35A3, SLC6A13, SPATA6, SPRED2, SPTLC1, STK17B, SULF1, TMEM90B, TRMT11, ULK2, WNT2B, ZAK, ZBTB17, ZNF224, ZNF350, ZNF665
  Subclade 2b, 124 synapomorphies
  ADAMTS7, ADRA1B, AGAP2, AK022254, AK024568, AMACR, AP2S1, ARHGDIG, ARHGEF16, ARSJ, ASAH1, ATF4, ATP5H, ATP5L, ATXN7L1, ATXN8OS, AV720803, BAT2, BAX, BGN, BID, BRD2, C7orf28B, CABIN1, CAPZB, CASS4, CCDC88C, CCK, CD58, CDCA4, CDKN2A, CHIT1, CKAP4, COG8, CRCP, CRELD2, CTNNBL1, CYP27B1, CYP2R1, D25272, DGCR8, DRD1, DYSF, EDN2, EHMT2, FGD1, FRS2, FSHB, GALK1, GALNT2, GGCX, GIPR, GLRX3, GNAS, GOLGA2, GPR135, GRHPR, HDLBP, HLA-DOB, HSDL2, HSP90B1, IDH2, IL17B, IL1A, IRAK1, KCNG2, KIAA0319, KIAA1045, KIF1C, KLC1, KLHL20, LANCL2, LMNA, LOC440792, LRCH4, LYZL6, MAP4, MARCO, MDK, MECR, MFNG, NCOR2, NCRNA00260, NFU1, NPHS1, NRIP2, NUP50, OVOL1, P2RY2, PDCD5, PECR, PFDN2, PFN1, PLAUR, PLK3, POLD1, POLR1E, POM121C, PTGIR, PTPLAD1, PUM1, RARG, RFC2, RNF126, RPL22P22, RRP7B, SH3BP2, SLC7A5, SNRPB2, SPIN2A, TGM5, TM9SF1, TMEM132A, TMEM134, TPM4, TSSC1, TUBG1, TXN, UBE2V1P2, UBR4, VEGFA, VENTX, WDR18, Z21967
  Subclade 2c–e, 48 synapomorphies
  AA427737, ADORA1, AF257099, AL137403, BCLAF1, CA3, CCL2, CFLAR, CXCL2, CXCR4, CYLD, DKFZp686O1327, EIF4A1, FKBP8, FRMD1, FUT6, GPR183, GTF2F1, HEY2, IFNGR1, IGHV4-31, KIAA0020, MCL1, MLF1, MYH14, NCLN, NDRG2, NUP88, PDE4B, PNLIPRP2, PPP1R15A, PRNP, PTMA, PTMAP7, PTPN21, RGS1, RNF114, SEC24A, SFRP1, SRF, SRGN, TNFAIP2, TRIM2, UPF3A, WASF3, WSB1, YWHAH, ZFP36

Clade 3
5 Specimens: all from HNTDI
GSM242016, GSM242019, GSM242020, GSM242021, GSM512560
44 Synapomorphies:
ACTR10, ALDH1A3, C14orf147, CAPZA1, CD59, CHMP1B, COPS8, CPD, CSDE1, DCUN1D4, GALNT1, GCOM1, GMFB, HSPH1, KRT10, LEPROTL1, LOC440366, LYST, MCL1, NCRNA00081, NCRNA00120, NUDT4P1, NUPL1, PDS5A, PTP4A1, RAP1A, RBBP7, RBM16, RRAS2, RRP15, SCARB2, SCML1, SET, SLC25A14, SMEK2, SNRNP27, SNRPE, SNX27, SOCS5, YRDC, YWHAZ, ZFP36L1, ZMPSTE24, ZSCAN18

Clade 4
11 Specimens: all from RM
GSM242009, GSM242013, GSM512540, GSM512543, GSM512547, GSM512549, GSM512550, GSM512551, GSM512552, GSM512554, GSM512556
6 Synapomorphies:
DSCAM, DUSP1↑, EIF1↑, HIST1H2BC, JUN, SIK1
  Subclades 4a, b, 17 synapomorphies
  ACAT2, ACBD3, ADAR, ARL4C, BRD7, CAPZB, KATNA1, MRPL39, NEDD8, NSMCE4A, PBX1, PEX19, PTP4A2, SF3A3, SSBP1, TDRD7, WBP4
  Subclades 4c, 17 synapomorphies
  AF198444, AK021633, CITED2, DCUN1D4, DUSP7, FILIP1L, GATM, HIST2H2AA4, HIST2H2AA4, HSPC157, KLF6, NEAT1, PNRC1, REG1A, RHOB, SLC38A2, TOP3A