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Table 1 List of 48 genes commonly upregulated in human iPS cells and human iPS-beating clusters (BCs) as compared to, respectively, human ES cells and human ES-BCs.

From: Global transcriptional profiles of beating clusters derived from human induced pluripotent stem cells and embryonic stem cells are highly similar

Symbol1

Mean ES

Mean ES-BC

p-value2 (ES vs ES-BC)

Mean iPS

Mean iPS-BC

p-value2 (iPS vs iPS-BC)

Fold change iPS-BC/ES-BC

Overlap3

ADFP

94

118

> 0,05

2125

1490

> 0,05

12,6

-

ANGEL2

510

430

> 0,05

1181

1198

> 0,05

2,8

-

B3GALNT1

81

78

> 0,05

386

443

> 0,05

5,7

-

C1orf176

95

94

> 0,05

229

231

> 0,05

2,5

-

CFLAR

120

92

> 0,05

294

215

> 0,05

2,3

Chin-E

CKLF

417

290

> 0,05

921

582

> 0,05

2,0

-

COMT

257

194

> 0,05

1172

1958

> 0,05

10,1

Chin-E; Marchetto

CYorf15A

123

94

> 0,05

566

407

> 0,05

4,3

-

CYorf15B

78

85

> 0,05

237

189

> 0,05

2,2

-

DNAJC15

112

179

> 0,05

504

402

> 0,05

2,2

Chin-E

EIF1AY

75

77

> 0,05

1569

2114

> 0,05

27,5

-

EPSTI1

155

136

> 0,05

345

651

> 0,05

4,8

Chin-E

HLA-B

203

158

> 0,05

614

513

> 0,05

3,2

Chin-E

IRAK1

97

92

> 0,05

511

480

> 0,05

5,2

-

JARID1D

83

79

> 0,05

407

489

> 0,05

6,2

-

LEMD3

516

480

> 0,05

1382

1278

> 0,05

2,7

-

MAP1LC3A

76

91

> 0,05

753

1276

> 0,05

14,0

Chin-E

MEIS3P1

87

112

> 0,05

305

362

> 0,05

3,2

-

MGC3207

430

299

> 0,05

1040

757

> 0,05

2,5

-

MGMT

83

76

> 0,05

453

405

> 0,05

5,3

-

MNS1

89

93

> 0,05

325

217

> 0,05

2,3

-

NAPRT1

196

190

> 0,05

679

382

> 0,05

2,0

-

NLGN4Y

79

80

> 0,05

385

325

> 0,05

4,1

-

NME4

89

127

> 0,05

7001

5461

> 0,05

43,0

Chin-L; Marchetto

OXCT1

90

94

> 0,05

272

358

> 0,05

3,8

-

PTGR1

84

79

> 0,05

1613

1290

> 0,05

16,3

Chin-E

PUS7L

92

82

> 0,05

327

211

> 0,05

2,6

-

RPS4Y1

86

96

> 0,05

4190

4645

> 0,05

48,4

-

SLC39A8

86

91

> 0,05

263

269

> 0,05

3,0

Marchetto

SPIN3

84

96

> 0,05

335

206

> 0,05

2,1

-

TFCP2

355

190

> 0,05

765

466

> 0,05

2,5

-

TMBIM4

223

232

> 0,05

1848

1545

> 0,05

6,7

Chin-L

TRIM4

87

79

> 0,05

307

340

> 0,05

4,3

-

TSPYL5

79

82

> 0,05

296

350

> 0,05

4,3

Chin-E, L

ZNF167

89

76

> 0,05

262

232

> 0,05

3,1

Marchetto

ZNF22

123

256

0,0003

1807

1311

> 0,05

5,1

-

ZNF248

95

76

> 0,05

202

212

> 0,05

2,8

Chin-E

ZNF626

79

77

> 0,05

196

239

> 0,05

3,1

-

CXCL12

399

958

> 0,05

815

1782

0,0245

1,9

-

DYNLT3

82

96

> 0,05

227

455

0

4,7

Chin-E

GGCT

92

179

> 0,05

1908

836

0,0007

4,7

-

GRTP1

85

82

> 0,05

571

201

0

2,5

-

PHF11

79

79

> 0,05

651

307

0

3,9

-

PRKAR1A

83

83

> 0,05

651

1357

0,0003

16,3

-

RPL39L

977

155

0

2352

668

0

4,3

-

ZNF280D

78

78

> 0,05

511

178

0,0138

2,3

Chin E

KDELR3

79

92

> 0,05

185

488

0,0004

5,3

Chin-E

RPL39L

221

107

> 0,05

997

280

0

2,6

-

      

Mean ± SD

6,9 ± 9,4

 
  1. 1 Genes with names depicted in bold are expressed at similar levels in iPS cells and iPS cell-derived beating clusters (iPS-BCs).
  2. 2 The p-value of > 0.05 indicates that the differences in gene expression levels in comparisons iPS vs iPS-BC and ES vs ES-BC was not statistically significant. For differentially expressed genes in these comparisons the exact p-value is indicated. All genes in this table were differentially expressed (p < 0.05, > 2-fold change) in comparisons iPS vs ES and iPS-BC vs ES-BC.
  3. 3 Overlap with iPS cell-specific genes reported by Chin et al. [29] and/or Marchetto et al. [31] is indicated. Two genes (NME4 and COMT) in this table were reported to be overexpressed in human iPS cells by both groups. One gene (TSPYL5) from our list was reported to be overexpressed in both early and late passage iPS cells by Chin et al. ("Chin-E, L"). The gene TMBIM4 was found to be overexpressed only in late passage iPS cells (three different cell lines) by Chin et al. ("Chin-L"). All other probe sets in this table were detected only in early passage iPS cells (five different cell lines) by Chin et al. ("Chin-E").