Suppl. Table S3. Sarcoma gene expression signature shared by mouse Kras; p16p19null sarcomas and human RMS.

Probe Set ID Gene Symbol Gene title

Previously published association with

malignanciesReferences

207173_x_atCDH11

cadherin 11, type 2, OB-cadherin

(osteoblast)

CDH11 expression predicts survival in

patients with osteosarcoma.

Nakajima et al., 2007(1)

207172_s_at

209891_at SPC25

SPC25, NDC80 kinetochore

complex component, homolog (S. cerevisiae)

214452_at BCAT1branched chain

aminotransferase 1, cytosolic

Assciated with metastatic

medulloblastoma and chemotherapy-resistant

ovarian cancer.

De Bont et al., 2008; Ju et al., 2009

(2, 3)

206432_at HAS2 hyaluronan synthase 2

Expression of Has2 in highly invasive breast

cancer cell lines; HAS2 transfection of

fibrosarcoma cell line HT-1080 results in

enhanced tumorigenicity and anchorage-

independent growth.

Udabage etal., 2005; Kosaki et al., 1999

(4, 5)

218542_at CEP55 centromere protein E, 312kDa

Association with head and neck squamous cell carcinoma progression

Waseem et al., 2010(6)

212158_at SDC2 syndecan 2

Prognostic factor in esophagus carcinoma;

Increased expression in colon carcinoma cell

lines.

Huang et al., 2009; Han et al., 2004

(7, 8)

209647_s_at SOCS5 suppressor of High SOCS5 levels in Evans et al., 2007

cytokine signaling 5 breast cancer cell lines. (9)

202935_s_atSOX9

SRY (sex determining

region Y)-box 9

Associated with human soft-tissue

maliganncies

Soederstroem et al., 2002; Cajaiba et al.,

2010(10, 11)202936_s_at

211121_s_at DOK1

docking protein 1, 62kDa

(downstream of tyrosine kinase 1)

Functions as a tumor suppresor in the

hematopoietic system

Niki et al., 2004(12)

204463_s_at

EDNRA endothelin receptor type A204464_s_at

216235_s_at

203313_s_at TGIF1TGFB-induced

factor homeobox 1

201897_s_at CKS1BCDC28 protein

kinase regulatory subunit 1B

Associated with adverse outcomes in human

hepatocellular carcinoma, cutaneous

squamous cell carcinoma, multiple

myeloma.

Huang et al., 2010; Salgado et al., 2010; Chang et al., 2010

(13-15)

213506_at F2RL1coagulation factor

II (thrombin) receptor-like 1

210933_s_at

FSCN1

fascin homolog 1, actin-bundling

protein (Strongylocentrot

us purpuratus)

Correlates with progression/ adverse

outcomes in human non small cell lung cancer,

nasopharyngeal/ hepatocellular/

urothelial carcinoma.

Zhao et al., 2010; Wu et al., 2010; Iguchi et

al., 2009; Tong et al.,2005(16-20)201564_s_at

218009_s_at PRC1 protein regulator of cytokinesis 1

Upregulated in leiomyosarcoma

Skubitz and Skubitz, 2003 (21)

201666_at TIMP1TIMP

metallopeptidase inhibitor 1

Low serum levels in patients with high-

grade soft-tissue sarcomas; Induction of

TIMP1 in a fibrosarcona cell line (HT1080) suppresses

invasive potential.

Benassi et al., 2003; Tanaka et al., 1995

(22, 23)

203625_x_at SKP2S-phase kinase-

associated protein 2 (p45)

Target gene in PAX3-FKHR positive

rhabdomyosarcoma

Nishijo et al., 2009(24)

204026_s_at ZWINT ZW10 interactor

210495_x_at

FN1 Fibronectin

Increased Fibronectin-dependent

proliferation, adhesion and invasion of human fibrosarcoma cell line HT1080; Correlates

with disease progression in human renal cell carcinoma.

Waalkes et al., 2010(25)

211719_x_at

212464_s_at

214701_s_at

214702_at

216442_x_at

209832_s_at CDT1

chromatin licensing and

DNA replication factor 1

Highly expressed in human neoplastic

lesions of the colon

Bravou et al., 2005(26)

203418_at

CCNA2 cyclin A2 Associated with chemotherapy-resistant

ovarian cancer.

Ju et al., 2009(3)

213226_at

208712_atCCND1 cyclin D1

208711_s_at

204244_s_at DBF4 DBF4 homolog (S. cerevisiae)

CDC7-DBF4 overexpression in

various human malignancies.

Bonte et al., 2008(27)

204033_at TRIP13thyroid hormone

receptor interactor 13

Genomic copy number changes in early stages of non small cell lung

cancer.

Kang et al., 2008(28)

213139_at SNAI2 snail homolog 2 (Drosophila)

Mediates invasiveness in human gliomas and

prostate cancer cell lines.

Emadi et al., 2010; Yang et al., 2010

(29, 30)

207466_at GAL galanin prepropeptide

Putative biomarker in human squamous cell

carcinoma

Sugimoto et al., 2009.(31)

205249_at EGR2 early growth response 2

Induces apoptosis in various cancer cell lines

Unoki and Nakamura, 2003 (32)

201631_s_at IER3 immediate early response 3

Association with pancreatic

adenocarcinoma; stress-inducible protein

regulating cell proliferation/ apoptosis.

Sasada et al., 2008(33)

203111_s_at PTK2BPTK2B protein

tyrosine kinase 2 beta

Stimulates glioma cell migration

Lipinski et al., 2005(34)

206115_at EGR3 early growth response 3

Predictive of adverse outcome in human

breast cancer

Suzuki et al., 2007(35)

208621_s_at EZR ezrin Upregulated in osteosarcoma

compared to benign bone tumors; Linked

to the metastatic behavior of

rhabdomyosarcoma.

Wan et al., 2009; Yu et al., 2004

(23, 36)

211564_s_at

PDLIM4 PDZ and LIM domain 4

Reduces prostate cancer cell growth

Vanaja et al., 2009(37)218691_s_at

214175_x_at

217997_atPHLDA1

pleckstrin homology-like

domain, family A, member 1

Downregulation in prognostically poor breast cancer and

metastatic melanoma.

Nagai et al., 2007; Neef et al., 2002

(38, 39)217999_s_at

201286_at

SDC1 syndecan 1

Expression in epitheloid sarcoma, synovial sarcoma, GIST, malignant

schwannoma; Transfection of

fibrosarcoma cell line HT-1080 results in

increased growth rate and more lung

metastases.

Orosz and Kopper, 2001; Peterfia et al.,

2006(40, 41)201287_s_at

213100_at UNC5B Unc-5 homolog B (C. elegans)

221269_s_at SH3BGRL3

SH3 domain binding glutamic acid-rich protein

like 3

205047_s_at ASNS asparagine synthetase

New biomarker in ovarian cancer.

Lorenzi and Weinstein, 2009 (42)

219148_at PBK PDZ binding kinase EWS/ FLI1 target Herrero-Martin et al.,

2009 (43)

201930_at MCM6 minichromosome maintenance

complex component 6

MCM6 identifies progressive

chondrosarcoma

Helfenstein et al., 2004(44)

208808_s_at HMGB2 high-mobility group box 2

Expression correlates with progression of

squamous cell carcinoma of the skin.

Sharma et al., 2008(45)

212836_at POLD3

polymerase (DNA-directed), delta 3, accessory

subunit

205628_at PRIM2primase, DNA, polypeptide 2

(58kDa)

205180_s_at ADAM8ADAM

metallopeptidase domain 8

ADAM8 expression crrelates with

invasiveness in human pancreatic cancer, prostate cancer and

brain tumors.

Mochizuki and Okada, 2007; Valkovskaya et al., 2007; Fritzsche et

al., 2006; Wildeboer et al., 2006 (46-49)

202052_s_at RAI14 retinoic acid induced 14

209505_atNR2F1

Nuclear receptor subfamily 2,

group F, member 1209506_s_at

219117_s_atFKBP11

FK506 binding protein 11, 19

kDa219118_at

208258_s_at GAS2L1growth arrest-

specific 2 like 1Diminuished expression levels in acute myeloid

leukemia

Desmond et al., 2007(50)

200698_at KDELR2 KDEL(Lys-Asp-Glu-Leu)

endoplasmic reticulum protein retention receptor

2

200699_at

200700_s_at

201862_s_atLRRFIP1

leucine rich repeat (in FLII)

interacting protein 1211452_x_at

212364_at MYO1B myosin IB

208452_x_atMYO9B myosin IXB

217297_s_at

216804_s_at PDLIM5 PDZ and LIM domain 5

206636_at RASA2 RAS p21 protein activator 2

209146_at SC4MOL sterol-C4-methyl oxidase-like

201920_at SLC20A1

solute carrier family 20

(phosphate transporter), member 1

202088_at SLC39A6

solute carrier family 39 (zinc

transporter), member 6

Breast-cancer associated protein

Taylor et al., 2003(51)

213164_at SLC5A3

solute carrier family 5 (sodium/

myoinositol cotransporter),

member 3

209218_at SQLE squalene epoxidase

Potential biomarker in human prostate cancer,

Zhao et al., 2010; Harada et al., 2009;

pancreatic adenocarcinoma, breast

cancer.

Helms et al., 2008(52-54)

213562_s_at

213577_at

203476_at TPBG trophoblast glycoprotein

Upregulated in gastrointestinal stromal tumors

Gromova et al., 2009(55)

209191_at TUBB6 tubulin, beta 6

201397_at PHGDH phosphoglycerate dehydrogenase

High expression associated with adverse

outcome in breast cancer

Pollari et al., 2010(56)

219161_s_atCKLF chemokine-like

factor221058_s_at

206704_at CLCN5 chloride channel 5

207030_s_atCSRP2

cysteine and glycine-rich

protein 2

Expressed in hepatocellular

carcinoma.

Midorikawa et al., 2002(57)

211126_s_at

214074_s_at CTTN cortactin

Cortactin staining in rhabdomyosarcomas, leiomyosarcomas, one infantile fibrosarcoma

and one MFH.

Parham et al., 1995(58)

201095_at DAP death-associated protein

203279_at EDEM1

ER degradation enhancer,

mannosidase alpha-like 1

206501_x_at ETV1 ets variant 1 Rare EWS fusions in Ewings family tumors Wang et al., 2007

include two EWS/ETV1 fusions. (59)

217053_x_at

217061_s_at

221910_at

221911_at

207178_s_at FRK fyn-related kinase

Associates with Rb; Functions as a tumor

suppressor in mammary epithelial cells by

regulating PTEN protein stability and function.

Craven et al., 1995; Yim et al., 2009

(60, 61)

204472_at GEM

GTP binding protein

overexpressed in skeletal muscle

208460_at GJC1gap junction

protein, gamma 1, 45kDa

214472_at HIST1H2AD histone cluster 1, H2ad

200644_at MARCKSL1 MARCKS-like 1 Expression in prostate cancer

Romanuik et al., 2009(62)

203228_at PAFAH1B3

platelet-activating factor

acetylhydrolase, isoform Ib,

subunit 3 (29kDa)

207505_at PRKG2protein kinase,

cGMP-dependent, type II

203423_at RBP1 retinol binding protein 1, cellular

204336_s_at RGS19 regulator of G-protein signaling

19

219493_at SHCBP1 SHC SH2-domain binding protein 1

37831_at SIPA1L3signal-induced proliferation-

associated 1 like 3

212944_at SLC5A3

solute carrier family 25

(mitochondrial carrier; phosphate carrier), member

24

204619_s_at

VCAN versican

Contributes to cancer invasion and

mestastasis; expressed in human epithelial

cancers.

Ricciardelli et al., 2009(63)

204620_s_at

215646_s_at

221731_x_at

209765_at ADAM19

ADAM metallopeptidase

domain 19 (meltrin beta)

Upregulated in brain tumors

Wildeboer et al., 2006(49)

219693_at AGPAT4

1-acylglycerol-3-phosphate O-

acyltransferase 4 (lysophosphatidic

acid acyltransferase,

delta)

202207_atARL4C ADP-ribosylation

factor-like 4C

202208_s_at

203404_at ARMCX2armadillo repeat containing, X-

linked 2

200920_s_at BTG1

B-cell translocation gene

1, anti-proliferative

Bcl-2-regulated mediator of apoptosis in

breast cancer cells

Nahta et al., 2006(64)

201850_at CAPGcapping protein (actin filament),

gelsolin-like

Linked to motility of pancreatic cancer cells;

Expressed in serous ovarian

adenocarcinomas.

Thompson et al., 2007; Partheen et al., 2008

(65, 66)

218802_at CCDC109Bcoiled-coil

domain containing 1

210821_x_at CENPA centromere protein A

CENPA overexpression promotes genome instability in pRb-

depleted human cells.

Amato et al, 2009(16)

203044_at CHSY1 chondroitin sulfate synthase 1

217025_s_at DBN1 drebrin 1

202719_s_at TEStestis derived

transcript (3 LIM domains)

Putative tumor suppressor in human

epithelial, hematopoietic malignancies and

human glioblastoma.

Gunduz et al., 2009; Mueller et al., 2007; Drusco et al., 2005; Chene et al., 2004

(67-70)

213253_at SMC2structural

maintenance of chromosomes 2

204222_s_at GLIPR1 GLI pathogenesis-related 1

209372_x_at TUBB2A tubulin, beta 2A

205122_at TMEFF1 transmembrane protein with EGF-

like and two follistatin-like

Gery et al., 2003(71)

domains 1

As

201952_atALCAM

activated leukocyte cell

adhesion molecule

Association with breast cancer; Expression in

pancreatic adenocarcinoma

predicts worse outcome.

Davies et al., 2008; Kahlert et al., 2009

(72, 73)201951_at

204962_s_at CENPA centromere protein A

CENPA overexpression promotes genome instability in pRb-

depleted human cells.

Amato et al, 2009(16)

204170_s_at CKS2

CDC28 protein kinase

regulatory subunit 2

Upregulated in leiomyosarcomas

Skubitz and Skubitz, 2003 (21)

204558_at RAD54L RAD54-like (S. cerevisiae)

205046_at CENPE centromere protein E, 312kDa

Expressed in neuroblastoma, regulates cell proliferation;

Upregulated in chemoresistant ovarian

cancer.

Balamuth et al., 2010; Ju et al., 2009

(3, 74)

202870_s_at CDC20cell division cycle

20 homolog (S. cerevisiae)

High levels of CDC20 associated with poor outcomes in ovarian

cancer

Ouellet et al., 2006(75)

207143_at CDK6 cyclin-dependent kinase 6

Inhibition of cyclin-dependent kinase 4/6

activity arrests proliferation in

myoblasts/ rhabdomyosarcoma-

derived cells.

Saab et al., 2006(76)

220085_at HELLS helicase, lymphoid-specific

Potential serum marker for melanoma

metastasis; Association with head and neck

squamous cell carcinoma.

Kim et al., 2010; Waseem et al., 2010

(6, 77)

203344_s_at RBBP8 retinoblastoma binding protein 8

201291_s_atTOP2A

topoisomerase (DNA) II alpha

170kDa

Upregulated in leiomyosarcomas

Skubitz and Skubitz, 2003 (21)

201292_at

212345_s_at CREB3L2AMP responsive element binding protein 3-like 2

FUS-CREB3L1/L2 fusion in low-grade

myoxoid fibrosarcoma

Matsuyama et al., 2006 (78)

203028_s_at CYBAcytochrome b-

245, alpha polypeptide

204137_at GPR137B G protein-coupled receptor 137B

220063_at GSTCD

glutathione S-transferase, C-

terminal domain containing

200618_at LASP1 LIM and SH3 protein 1

Upregulated in human breast cancer, ovarian cancer, bladder cancer,

medulloblastoma; Linked to cell

proliferation, migration and metastasis.

Traenka et al., 2010; Chiyomaru et al., 2010; Grunewald et al., 2007;

Asaka et al., 2006(79-82)

221011_s_at LBHlimb bud and heart development homolog (mouse)

212843_at NCAM1neural cell adhesion

molecule 1

Nearly ubiquitous NCAM in alveolar

rhabdomyosarcoma; NCAM expression in synovial sarcomas;

Bahrami et al, 2008; Hartel et al, 2007;

Molenaar and Muntinghe, 1998

NCAM widely expressed in

(83-85)

217963_s_at NGFRAP1

nerve growth factor receptor (TNFRSF16)

associated protein 1

215743_at NMT2N-

myristoyltransferase 2

Potential chemoresistance gene

in osteosarcoma; Expression in human

brain tumors and human colon cancer.

Walters et al., 2008; Lu et al., 2005;

Selvakumar et al., 2006 (86-88)

204866_at PHF16 PHD finger protein 16

204944_at PTPRGprotein tyrosine

phosphatase, receptor type, G

Candidate tumor suppressor gene in

nasopharyngeal carcinoma

Cheung et al., 2008(89)

217775_s_atRDH11

retinol dehydrogenase 11 (all-trans/ 9-cis/

11-cis)217776_at

204342_at SLC25A24

solute carrier family 25

(mitochondrial carrier; phosphate carrier), member

24

204913_s_at SOX11SRY (sex

determining region Y)-box 11

Expressed in human malignant gliomas, medulloblastoma,

hematopoietic malignancies, ovarian

Weigle et al., 2005; De Bont et al., 2008;

Gustavsson et al., 2010; Brennan et al., 2009

cancer. Regulates cell growth.

(2, 90-92)

209118_s_at TUBA1A tubulin, alpha 1a

202391_at BASP1

brain abundant, membrane

attached signal protein 1

Reduced expression in hepatocellular

carcinoma

Moribe et al., 2008(93)

217985_s_at BAZ1Abromodomain

adjacent to zinc finger domain, 1A

208838_atCAND1

cullin-associated and neddylation-

dissociated 1207483_s_at

202806_at DBN1 drebrin 1

202539_s_atHMGCR

3-hydroxy-3-methylglutaryl-Coenzyme A

reductase202540_s_at

204886_atPLK4 polo-like kinase 4

(Drosophila)

Plk4 haploinsufficiency causes mitotic infidelity

and carcinogenesis

Ko et al., 2005(94)

204887_s_at

211181_x_at RUNX1runt-related transcription

factor 1

Most frequent target of chromosomal

rearrangements in human leukemia.

Lichtinger et al., 2010(95)

201645_at TNC tenascin C

Promotes survival of human

chondrosarcoma cells in vitro

Jang and Chung, 2005(96)

204995_at CDK5R1 cyclin-dependent kinase 5,

regulatory subunit 1 (p35)

210367_s_at PTGES prostaglandin E synthase

215813_s_at PTGS1

prostaglandin-endoperoxide

synthase 1 (prostaglandin G/H synthase

and cyclooxygenase)

Expressed in Kaposi's sarcomas

Rossiello et al., 2007(97)

200745_s_atGNB1

guanine nucleotide

binding protein (G protein), beta polypeptide 1

Decreased expression in unfavorable NB tumors

Thorell et al., 2009(98)

200746_s_at

218468_s_at GREM1

gremlin 1, cysteine knot superfamily,

homolog (Xenopus laevis)

Overexpression in human epithelial

tumors and sarcomas.

Namkoong et al., 2006(99)

202954_at UBE2Cubiquitin-

conjugating enzyme E2C

Upregulated in leiomyosarcomas

Skubitz and Skubitz, 2003 (21)

201250_s_at SLC2A1

solute carrier family 2

(facilitated glucose

transporter), member 1

Expression in human rhabdomyosarcoma

cell line RD; Expressed in 50% of

leiomyosarcomas, but not in leiomyomas.

Ito et al., 2000; Rao et al., 1999 (100, 101)

218399_s_at CDCA4 cell division cycle associated 4

201875_s_atMPZL1 myelin protein

zero-like 1210594_x_at

220892_s_at PSAT1 phosphoserine aminotransferase

Expressed in human colon tumors; PSAT1

Vie et al., 2008(102)

1

overexpression increases growth rate/

survival of colon carcinoma cell line.

204141_at TUBB2A tubulin, beta 2A

203440_at CDH2cadherin 2, type

1, N-cadherin (neuronal)

Expressed in human rhabdomyosarcoma; Expressed in human pleural mesothelioma

and melanoma.

Soler et al., 1993; Han et al., 1999; Attis et

al., 2006(103-105)

209081_s_at COL18A1 collagen, type XVIII, alpha 1

Expressed in osteosarcoma Kim et al., 2009 (106)

221059_s_at COTL1 coactosin-like 1 (Dictyostelium)

217992_s_at EFHD2EF-hand domain family, member

D2

206335_at GALNSgalactosamine (N-acetyl)-6-sulfate

sulfatase

209651_at TGFB1I1

transforming growth factor beta

1 induced transcript 1

205123_s_at TMEFF1

transmembrane protein with EGF-

like and two follistatin-like

domains 1

Putative tumor suppressor gene in

human brain cancers

Gery et al., 2003(71)

214085_x_at GLIPR1 GLI pathogenesis-related 1

204240_s_at SMC2structural

maintenance of chromosomes 2

202720_at TES testis derived transcript (3 LIM

Putative tumor suppressor in human

Gunduz et al., 2009; Mueller et al., 2007;

domains)epithelial, hematopoietic

malignancies and human glioblastoma.

Drusco et al., 2005; Chene et al., 2004

(67-70)

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