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. 2008 Sep;12(3):183–199. doi: 10.1089/omi.2008.0010

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