Table 2 Genes with a P-value of <0.001 in each comparison of RT vs non-RT, RT vs CMN, RT vs CCSK, RT vs WT, and with a fold change of >2 or <0.5 in the comparison between RT and non-RT

From: Rhabdoid tumor: gene expression clues to pathogenesis and potential therapeutic targets

Gene symbol

Description

Chromosome location

UniGene ID

Fold change RT vs non-RT

P-value RT vs non-RT

Genes associated with INI-1

 SMARCB1a

INI-1

22q11

534350

0.49

9.37E−21

 ATP1B1

ATPase, Na+/K+ transporting, β 1 polypeptide

1q24

291196

0.13

3.87E−19

 COL5A2

Collagen, type V, α 2

2q14–q32

445827

3.11

1.64E−10

 DOCK4a,b

Dedicator of cytokinesis 4

7q31.1

654652

0.40

8.11E−20

 NQO1

NAD(P)H dehydrogenase, quinone 1

16q22.1

406515

4.58

1.33E−06

 PLOD1

Procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1

1p36.3–p36.2

75093

2.17

7.27E−11

 PTNa

Pleiotrophin (heparin-binding growth factor 8)

7q33–q34

371249

0.33

6.74E−12

 PTP4A2

Protein tyrosine phosphatase type IVA, member 2

1p35

470477

2.14

7.47E−07

 PTPRKa,b

Protein tyrosine phosphatase, receptor type, K

6q22.2–q22.3

155919

0.22

3.76E−23

 RSU1b

Ras suppressor protein 1

10p13

524161

4.99

1.19E−05

 SPOCK1a

Sparc/osteonectin, (testican) 1

5q31

654695

0.25

4.85E−14

 SPP1b

Secreted phosphoprotein 1 (osteopontin)

4q21–q25

313

5.42

3.50E−07

 SERPINE2a

Serpin peptidase inhibitor, clade E,member 2

2q33–q35

38449

0.21

2.63E−09

Neural development

 CDH2

Cadherin 2, type 1, N-cadherin (neuronal)

18q11.2

464829

0.23

3.30E−06

 CITED2

Cbp/p300-interacting transactivator, 2

6q23.3

82071

0.47

1.93E−10

 CRIM1

Cysteine-rich transmembrane BMP regulator 1

2p21

332847

0.36

3.23E−15

 CXCL12

Chemokine (C-X-C motif) ligand 12

10q11.1

522891

0.27

1.14E−15

 DPYSL2

Dihydropyrimidinase-like 2

8p22–p21

173381

0.41

1.10E−04

 ENC1

Ectodermal-neural cortex

5q12–q13.3

104925

0.27

1.29E−16

 FSTL1

Follistatin-like 1

3q13.33

269512

0.29

4.35E−07

 FYN

FYN oncogene related to SRC, FGR, YES

6q21

390567

0.34

3.69E−15

 HES1

Hairy and enhancer of split 1 (Drosophila)

3q28–q29

250666

0.49

2.97E−07

 IGFBP2

Insulin-like growth factor binding protein 2

2q33–q34

438102

0.35

9.35E−08

 LAMA4

Laminin, α 4

6q21

654572

0.33

1.12E−05

 LAMB1

Laminin, β 1

7q22

650585

0.29

4.15E−10

 LEF1

Lymphoid enhancer-binding factor 1

4q23–q25

555947

0.21

8.22E−18

 LMO4

LIM domain only 4

1p22.3

436792

0.25

2.38E−16

 NAV2

Neuron navigator 2

11p15.1

502116

0.41

1.01E−11

 NCAM1

Neural cell adhesion molecule 1

11q23.1

503878

0.29

1.12E−18

 NOTCH2

Notch homolog 2 (Drosophila)

1p13–p11

487360

0.40

4.05E−11

 RND3

Rho family GTPase 3

2q23.3

6838

0.23

1.13E−12

 SOBP

Sine oculis binding protein homolog

6q21

445244

0.33

3.82E−06

 SOX11

SRY (sex determining region Y)-box 11

2p25

432638

0.19

2.76E−24

 SPON1

Spondin 1, extracellular matrix protein

11p15.2

643864

0.20

4.51E−13

 TSPAN5

Tetraspanin 5

4q23

591706

0.37

1.59E−17

MYC-C targets

 ABCE1

ATP-binding cassette, sub-family E, member 1

1q31.2 /// 4q31

571791

2.10

2.08E−08

 ACAT1

Acetyl-coenzyme A acetyltransferase 1

11q22.3–q23.1

232375

2.24

8.78E−08

 AHCY

S-adenosylhomocysteine hydrolase

20cen–q13.1

–

2.30

1.71E−06

 CORO1C

Coronin, actin-binding protein, 1C

12q24.1

696037

2.25

3.88E−05

 CYCS

Cytochrome c, somatic

7p15.2

437060

2.14

7.26E−06

 DDX21

DEAD (Asp-Glu-Ala-Asp) box polypeptide 21

10q21

696064

2.66

7.73E−10

 ENO2

Enolase 2 (γ, neuronal)

12p13

511915

2.59

1.67E−06

 MTHFD2

Methylenetetrahydrofolate dehydrogenase 2

2p13.1

469030

2.40

1.03E−09

 MYO1B

Myosin IB

2q12–q34

439620

0.40

1.44E−06

 NEFH

Neurofilament, heavy polypeptide 200kDa

22q12.2

198760

2.22

3.09E−07

 PAM

Peptidylglycine α-amidating monooxygenase

5q14–q21

369430

0.41

2.29E−08

 SLC39A14

Solute carrier family 39, member 14

8p21.3

491232

2.39

1.58E−06

 TFRCb

Transferrin receptor (p90, CD71)

3q29

529618

3.16

1.53E−09

Tumor supression, invasion, or metastasis

 COL18A1

Collagen, type XVIII, α 1 (endostatin)

21q22.3

517356

0.41

2.48E−13

 MMP12

Matrix metallopeptidase 12

11q22.3

1695

4.07

6.18E−05

 NCOA3

Nuclear receptor coactivator 3

20q12

592142

2.43

5.12E−06

 SELENBP1

Selenium-binding protein 1

1q21–q22

632460

0.44

9.15E−20

 TES

Testis derived transcript (3 LIM domains)

7q31.2

592286

0.41

1.97E−13

 ZNF217

Zinc-finger protein 217

20q13.2

155040

2.65

1.51E−05

Transcription regulation

 AFF1

AF4/FMR2 family, member 1

4q21

480190

0.39

7.15E−09

 ATF5

Activating transcription factor 5

19q13.3

9754

2.05

2.17E−04

 ATXN1

Ataxin 1

6p23

434961

0.44

5.25E−10

 BNIP3

BCL2/adenovirus E1B 19 kDa interacting protein 3

10q26.3

144873

2.40

1.65E−06

 CBX6

Chromobox homolog 6

22q13.1

592201

2.36

1.65E−10

 GPR177

G protein-coupled receptor 177

1p31.3

647659

0.37

1.46E−09

 GTF3A

General transcription factor IIIA

13q12.3–q13.1

445977

2.02

2.10E−09

 HIST1H2BK

Histone cluster 1, H2bk

6p21.33

437275

2.57

5.35E−08

 HOXA11

Homeobox A11

7p15–p14

249171

0.30

9.38E−17

 KHDRBS3

KH domain , RNA binding, signal transduction associated 3

8q24.2

444558

0.48

3.46E−06

 NRIP1

Nuclear receptor interacting protein 1

21q11.2

155017

0.44

2.26E−06

 SHOX

Short stature homeobox

Xp22.3;Yp11.3

105932

2.26

7.35E−05

 ZMIZ1

Zinc-finger, MIZ-type containing 1

10q22.3

193118

0.40

3.11E−09

Signal transduction

 PDE10A

Phosphodiesterase 10A

6q27

348762

0.23

5.21E−17

 DDEF2

Development and differentiation enhancing factor 2

2p25∣2p24

555902

0.43

1.88E−10

 DUSP4

Dual specificity phosphatase 4

8p12–p11

417962

0.48

6.89E−17

 FARP1

FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1

13q32.2

403917

0.43

6.83E−10

 GCG

Glucagon

2q36–q37

516494

24.89

2.51E−05

 GNAI1

Guanine nucleotide α inhibiting activity polypeptide 1

7q21

134587

0.33

3.40E−09

 GNG12

Guanine nucleotide-binding protein (G protein), γ 12

1p31.3

696244

0.42

3.05E−06

 IRS2

Insulin receptor substrate 2

13q34

442344

0.24

9.21E−20

 PLCB1

Phospholipase C, β 1 (phosphoinositide-specific)

20p12

431173

0.33

4.87E−13

 PSD3

Pleckstrin and Sec7 domain containing 3

8pter–p23.3

434255

0.45

4.76E−13

 RIN2

Ras and Rab interactor 2

20p11.22

472270

0.43

1.92E−07

Miscellaneous

 ALDH7A1

Aldehyde dehydrogenase 7 family, member A1

5q31

483239

3.45

2.93E−04

 APLP1

Amyloid β (A4) precursor-like protein 1

19q13.1

74565

2.64

1.53E−07

 B4GALT5

β 1,4-galactosyltransferase, polypeptide 5

20q13.1–q13.2

370487

2.04

3.45E−04

 BDH2

3-hydroxybutyrate dehydrogenase, type 2

4q24

124696

0.49

2.12E−07

 BLVRB

Biliverdin reductase B

19q13.1–q13.2

515785

2.14

1.42E−06

 BTBD3

BTB (POZ) domain containing 3

20p12.2

696121

0.44

5.95E−12

 C12orf24

Chromosome 12 open reading frame 24

12q24.11

436618

2.24

1.50E−08

 C18orf1

Chromosome 18 open reading frame 1

18p11.2

149363

0.46

6.59E−21

 C1orf9

Chromosome 1 open reading frame 9

1q24

204559

2.66

1.66E−06

 CHST1

Carbohydrate (keratan sulfate Gal-6) sulfotransferase 1

11p11.2–p11.1

104576

0.44

2.26E−12

 CHST2

Carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2

3q24

8786

0.37

1.36E−17

 COL4A2

Collagen, type IV, α 2

13q34

508716

0.26

5.75E−13

 DCHS1

Dachsous 1 (Drosophila)

11p15.4

199850

0.40

6.00E−07

 EMP3

Epithelial membrane protein 3

19q13.3

9999

2.14

7.03E−07

 FAM59A

Family with sequence similarity 59, member A

18q12.1

444314

0.45

1.03E−07

 FER1L3

Fer-1-like 3, myoferlin (C. elegans)

10q24

655278

4.77

5.83E−05

 FLJ13197

Hypothetical FLJ13197

4p14

29725

0.34

6.73E−17

 PLBD1

Putative phospholipase B-like 1 Precursor

12p13.1

131933

3.30

7.11E−10

 FXYD6

FXYD domain containing ion transport regulator 6

11q23.3

635508

0.36

3.64E−07

 GRB10

Growth factor receptor-bound protein 10

7p12–p11.2

164060

0.39

3.73E−13

 GLUL

Glutamate-ammonia ligase

1q31

518525

0.47

1.27E−04

 GYG1

Glycogenin 1

3q24–q25.1

477892

2.73

2.15E−05

 KIAA0644

Unknown

7p15.1

21572

0.19

8.59E−28

 LIMCH1

LIM and calponin homology domains 1

4p13

335163

0.39

1.27E−13

 NIT2

Nitrilase family, member 2

3q12.2

439152

2.08

5.12E−10

 PFDN4

Prefoldin subunit 4

20q13.2

91161

2.00

3.74E−05

 PGAM1

Phosphoglycerate mutase 1

10q25.3

592599

2.09

5.85E−08

 PLP2

Proteolipid protein 2

Xp11.23

77422

3.36

8.00E−12

 PLTP

Phospholipid transfer protein

20q12–q13.1

439312

2.79

9.52E−06

 PPP3CA

Protein phosphatase 3, catalytic subunit, α isoform

4q21–q24

435512

0.28

9.39E−07

 SEPT11

Septin 11

4q21.1

128199

0.48

1.34E−07

 SH3BP4

SH3-domain-binding protein 4

2q37.1–q37.2

516777

0.37

3.70E−10

 SNX10

Sorting nexin 10

7p15.2

571296

2.16

2.72E−05

 ST6GAL1

ST6 β-galactosamide α-2,6-sialyltranferase 1

3q27–q28

207459

0.43

1.24E−12

 TNNT1

Troponin T type 1 (skeletal, slow)

19q13.4

631558

5.14

5.14E−07

 TWF1

Twinfilin, actin-binding protein, homolog 1

12q12

189075

2.03

2.46E−04

  1. aAlso involved in neural development.
  2. bAlso involved in tumor invasion/metastasis.
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