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.
| 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 Genes with names depicted in bold are expressed at similar levels in iPS cells and iPS cell-derived beating clusters (iPS-BCs).
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 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").