Table 5.
A Clade Composed of All Leiomyosarcoma Specimens is Defined in Relation to Normal Specimens (GDS533)
| A. Overexpressed synapomorphic genes: | ||
| S78187 | CDC25B cell division cycle 25B | NS |
| U40343 | CDKN2D cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) | NS |
| X54942 | CKS2 CDC28 protein kinase regulatory subunit 2 | NS |
| X79353 | CDI1 GDP dissociation inhibitor 1 | NS |
| X14850 | H2AFX H2A histone family, member X | NS |
| U51127 | IRF5 interferon regulatory factor 5 | NS |
| U04209 | MFAP1 microfibrillar-associated protein 1 | NS |
| U43177 | MpV17 mitochondrial inner membrane protein | NS |
| U19796 | MRPL28 mitochondrial ribosomal protein L28 | OE |
| U37690 | POLR2L polymerase (RNA) II (DNA directed) polypeptide L, 7.6 kDa | NS |
| M22960 | PPGB protective protein for beta-galactosidase (galactosialidosis) | NS |
| U09210 | SLC18A3 solute carrier family 18 (vesicular acetylcholine), member 3 | NS |
| M86752 | STIP1 stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein) | OE |
| M26880 | UBC ubiquitin C | OE |
| U43177 | UCN urocortin | NS |
| B. Underexpressed synapomorphic genes: | ||
| M12963 | ADH1A alcohol dehydrogenase 1A (class I), alpha polypeptide | UE |
| HG3638-HT3849_s_at | Amyloid Beta (A4) Precursor Protein, Alt. Splice 2, A4(751) | NS |
| L28997 | ARL1 ADP-ribosylation factor-like 1 | NS |
| Z49269 | CCL14 chemokine (C—C motif) ligand 14 | UE |
| M92934 | CTGF connective tissue growth factor | UE |
| M74099 | CUTL1 cut-like 1, CCAAT displacement protein (Drosophila) | NS |
| M96859 | DPP6 dipeptidyl-peptidase 6 | UE |
| U94855 | EIF3S5 eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa | NS |
| L25878 | EPHX1 epoxide hydrolase 1, microsomal (xenobiotic) | NS |
| U60061-U69140 | FEZ2 fasciculation and elongation protein zeta 2 (zygin II) | NS |
| X67491 | GLUDP5 glutamate dehydrogenase pseudogene 5 | NS |
| HG4334-HT4604_s_at | Glycogenin | NS |
| X53296 | IL1RN interleukin 1 receptor antagonist | NS |
| X55740 | NT53 5′-nucleotidase, ecto (CD73) | UE |
| X78136 | PCBP2 poly(rC) binding protein 2 | UE |
| Z50194 | PHLDA1 pleckstrin homology-like domain, family A, member 1 | NS |
| J02902 | PPP2R1A protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform | NS |
| J03805 | PPP2CB protein phosphatase 2, catalytic subunit, beta isoform | NS |
| U25988 | PSG11 pregnancy specific beta-1-glycoprotein 11 | NS |
| M98539 | PTGDS prostaglandin D2 synthase 21kDa (brain) | UE |
| X54131 | PTPRB protein tyrosine phosphatase, receptor type, B | NS |
| M12174 | RHOB ras homolog gene family, member B | NS |
| HG1879-HT3521_at | RHOQ ras homolog gene family, member Q | NS |
| X98534 | VASP vasodilator-stimulated phosphoprotein | NS |
| X51630 | WT1 Wilms tumor 1 | UE |
| HG3426-HT3610_s_at | Zinc Finger Protein Hzf-16, Kruppel-Like, Alt. Splice 1 | NS |
| M92843 | ZFP36 zinc finger protein 36, C3H type, homolog (mouse) | UE |
| C. Dichotomously expressed synapomorphic genes: | ||
| U80226 | ABAT 4-aminobutyrate aminotransferase | NS |
| M14758 | ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 | NS |
| M95178 | ACTN1 actinin, alpha 1 | NS |
| U76421 | ADARB12 adenosine deaminase, RNA-specific, B1 (RED1 homolog rat) | NS |
| U46689 | ALDH3A2 aldehyde dehydrogenase 3 family, member A2 | NS |
| L34820 | ALDH5A1 aldehyde dehydrogenase 5 family, member A1 (succinate-semialdehyde dehydrogenase) | NS |
| M84332 | ARF1 ADP-ribosylation factor 1 | NS |
| D14710 | ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | NS |
| X84213 | BAK1 BCL2-antagonist/killer 1 | NS |
| U23070 | BAMBI BMP and activin membrane-bound inhibitor homolog (Xenopus laevis) | NS |
| M33518 | BAT2 HLA-B associated transcript 2 | NS |
| X61123 | BTG1 B-cell translocation gene 1, anti-proliferative | NS |
| S60415 | CACNB2 calcium channel, voltage-dependent, beta 2 subunit | NS |
| M19878 | CALB1 calbindin 1, 28 kDa | NS |
| L76380 | CALCRL calcitonin receptor-like | NS |
| M21121 | CCL5 chemokine (C—C motif) ligand 5 | NS |
| D14664 | CD302 CD302 molecule | NS |
| X72964 | CETN2 centrin, EF-hand protein, 2 | NS |
| U66468 | CGREF1 cell growth regulator with EF-hand domain 1 | NS |
| M63379 | CLU clusterin | NS |
| X52022 | COL6A3 collagen, type Vi, alpha 3 | UE |
| L25286 | COL15A1 collagen, type XV, alpha 1 | NS |
| S45630 | CRYAB crystallin, alpha B | NS |
| X95325 | CSDA cold shock domain protein A | NS |
| U03100 | CTNNA1 catenin (cadherin-associated protein), alpha 1, 102kDa | NS |
| X52142 | CTPS CTP synthase | NS |
| D38549 | CYFIP1 cytoplasmic FMR1 interacting protein 1 | NS |
| X64229 | DEK DEK oncogene (DNA binding) | NS |
| M63391 | DES desmin | UE |
| Z34918 | EIF4G3 eukaryotic translation initiation factor 4 gamma, 3 | NS |
| U97018 | EML1 echinoderm microtubule associated protein like 1 | NS |
| U12255 | FCGRT Fc fragment of IgG, receptor, transporter, alpha | NS |
| U36922 | FOXO1A forkhead box O1A (rhabdomyosarcoma) | NS |
| U91903 | FRZB frizzled-related protein | NS |
| M33197 | GAPDH glyceraldehyde-3-phosphate dehydrogenase | NS |
| U09587 | GARS glycyl-tRNA synthetase | NS |
| U66075 | GATA6 GATA binding protein 6 | NS |
| D13988 | GDI2 GDP dissociation inhibitor 2 | NS |
| U31176 | GFER growth factor, augmenter of liver regeneration (ERV1 homolog, S. cerevisiae) | NS |
| U28811 | GLG1 golgi apparatus protein 1 | NS |
| U66578 | GPR23 G protein-coupled receptor 23 | NS |
| L40027 | GSK3A glycogen synthase kinase 3 alpha | NS |
| U77948 | GTF2I general transcription factor II, i | UE |
| Z29481 | HAAO 3-hydroxyanthranilate 3,4-dioxygenase | NS |
| D16480 | HADHA hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit | NS |
| U50079 | HDAC1 histone deacetylase 1 | NS |
| U50078 | HERC1 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1 | NS |
| M95623 | HMBS hydroxymethylbilane synthase | NS |
| X79536 | HNRPA1 heterogeneous nuclear ribonucleoprotein A1 | NS |
| L15189 | HSPA9B heat shock 70 kDa protein 9B (mortalin-2) | NS |
| U05875 | IFNGR2 interferon gamma receptor 2 (interferon gamma transducer 1) | NS |
| X57025 | IGF1 insulin-like growth factor 1 (somatomedin C) | UE |
| HG3543- | IGF2 insulin-like growth factor 2 (somatomedin A) | NS |
| U40282 | ILK integrin-linked kinase | NS |
| X74295 | ITGA7 integrin, alpha 7 | NS |
| X57206 | ITPKB inositol 1,4,5-trisphosphate 3-kinase B | NS |
| AB002365 | KIAA0367 | UE |
| J00124 | KRT14 keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner) | NS |
| X05153 | LALBA lactalbumin, alpha- | NS |
| X02152 | LDHA lactate dehydrogenase A | NS |
| HG3527-HT3721_f_at | LHB luteinizing hormone beta polypeptide | NS |
| X86018 | LRRC41 leucine rich repeat containing 41 | NS |
| L38486 | MFAP4 microfibrillar-associated protein 4 | NS |
| D87742 | MIA3 melanoma inhibitory activity family, member 3 | NS |
| M69066 | MSN moesin | NS |
| AB003177 | mRNA for proteasome subunit p27 | NS |
| U47742 | MYST3 MYST histone acetyltransferase (monocytic leukemia) 3 | NS |
| M30269 | NID1 nidogen 1 | NS |
| U80669 | NKX3-1 NK3 transcription factor related, locus 1 (Drosophila) | NS |
| M10901 | NR3C1 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) | NS |
| M16801 | NR3C2 nuclear receptor subfamily 3, group C, member 2 | NS |
| U52969 | PCP4 Purkinje cell protein 4 | UE |
| J03278 | PDGFRB platelet-derived growth factor receptor, beta polypeptide | NS |
| D37965 | PDGFRL platelet-derived growth factor receptor-like | NS |
| Z49835 | PDIA3 protein disulfide isomerase family A, member 3 | NS |
| U78524 | PIAS1 protein inhibitor of activated STAT, 1 | NS |
| U60644 | PLD3 phospholipase D family, member 3 | NS |
| D11428 | PMP22 peripheral myelin protein 22 | NS |
| U79294 | PPAP2B phosphatidic acid phosphatase type 2B | NS |
| S71018 | PPIC peptidylprolyl isomerase C (cyclophilin C) | NS |
| X07767 | PRKACA protein kinase, cAMP-dependent, catalytic, alpha | NS |
| X83416 | PRNP prion protein (p27-30) | NS |
| M555671 | PROZ protein Z, vitamin K-dependent plasma glycoprotein | NS |
| U72066 | RBBP8 retinoblstoma binding protein 8 | NS |
| L25081 | RHOC ras homolog gene family, member C | NS |
| U40369 | SAT1 spermidine/spermine N1-acetyltransferase 1 | NS |
| M97287 | SATB1 special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNAs) | NS |
| U83463 | SDCBP syndecan binding protein (syntenin) | NS |
| U28369 | SEMA3B sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B | NS |
| HG3925-ht4195_at | SFTPA2 surfactant, pulmonary-associated protein A2 | NS |
| L31801 | SLC16A1 solute carrier family 16, member 1 (monocarboxylic acid transporter 1) | NS |
| M91463 | SLC2A4 solute carrier family 2 (facilitated glucose transporter), member 4 | NS |
| U66617 | SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | NS |
| U50383 | SMYD5 SMYD family member 5 | NS |
| D43636 | SNRK SNF related kinase | NS |
| D87465 | SPOCK2 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2 | NS |
| M61199 | SSFA2 sperm specific antigen 2 | NS |
| U15131 | ST5 suppression of tumorigenicity 5 | NS |
| U95006 | STRA13 stimulated by retinoic acid 13 homolog (mouse) | NS |
| M74719 | TCF4 transcription factor 4 | NS |
| X14253 | TDGF1 teratocarcinoma-derived growth factor 1 | NS |
| U52830 | TERT telomerase reverse transcriptase | NS |
| U12471 | THBS1 thrombospondin 1 | NS |
| U16296 | TIAM1 T-cell lymphoma invasion and metastasis 1 | NS |
| L01042 | TMF1 TATA element modulatory factor 1 | NS |
| U03397 | TNFRSF9 tumor necrosis factor receptor subfamily, member 9 | NS |
| X05276 | TMP4 tropomyosin 4 | UE |
| HG4683-HT5108_s_at | TRAF2 TNF receptor-associated factor 2 | NS |
| U64444 | UFD1L ubiquitin fusion degradation 1 like (yeast) | NS |
| U39318 | UBE2D3 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast) | NS |
| X59739 | ZFX zinc-finger protein, X-linked | NS |
Last column reports the status of the synapomorphies as described by Quade et al. (2004) in their significant genes list