Table 1. Comparison of human reprogramming experiments with a focus on ES/iPS comparison.
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| Starting cell type | Neonatal foreskin fibroblasts and fibroblasts differentiated from iPS | Primary fibroblasts: BJ and NHDF | Neonatal foreskin fibroblasts | Foreskin keratinocytes | Adult foreskin fibroblasts, fetus skin fibroblasts | Fibroblasts from a type 1 SMA patient and his unaffected mother | Foreskin fibroblasts | Parkinson disease patients dermal fibroblasts |
| Factors used | - Oct4, Sox2, c-Myc, Klf4- Oct4, Sox2, c-Myc, Klf4, Nanog | Oct4, Sox2, Klf4, Valproic acid (VPA) | Oct4, Sox2, c-Myc, Klf4, Nanog | Oct4, Sox2, c-Myc, Klf4 | Oct4, Sox2,Klf4, c-Myc, Utf1, P53si | Oct4, Sox2, Lin28, Nanog | Oct4, Sox2, Nanog, Lin28, c-Myc, Klf4, SV40LT | Oct4, Sox2, c-Myc, Klf4 |
| Vector used | DOX-inducible lentivirus | Retrovirus | Retrovirus | Retrovirus | Lentivirus | Lentivirus | oriP/EBNA1-based episomal vector with IRES2 | Excisable DOX-indusible lentivirus |
| Platform | Affy HG-U133 plus 2.0 (GPL570) | Illumina Human Ref-8 | Affy HG-U133 plus 2.0 (GPL570) | Affy HG-U133 plus 2.0 (GPL570) | Phalanx Human one aray (GPL6254) | Affy HG-U133 plus 2.0 (GPL570) | Affy HG-U133 plus 2.0 (GPL570) | Affy HG-U133 plus 2.0 (GPL570) |
| GEO accession number | GSE12390 | Pers. Comm | GSE9865 | GSE12583 | GSE12922 | GSE13828 | GSE15148 | GSE14711 |
| Corr coeff whole array iPS/ES: average (min-max) | Primary iPS: 0.988 (0.984–0.989) Secondary iPS: 0.991 (0.990–0.991) | 0.970 (0.950–0.980) | Part-iPS: 0.946 (0.928–0.962)iPS: 0.964 (0.953–0.976) | 0.956 (0.950–0.964) | Pre-iPS: 0.728 (0.730–0.812)iPS: 0.887 (0.832–0.923) | 0.973 (0.967–0.979) | 0.970 (0.960–0.978) | Integrated: 0.969 (0.965–0.972)Excised: 0.972 (0.969–0.977) |
| Corr coeff 316 biv domain genes | Primary iPS: 0.961 Secondary iPS: 0.970 | 0.974 | Part-iPS: 0.814 iPS: 0.885 | 0.949 | Pre-iPS: 0.497 iPS: 0.881 | 0.985 | 0.979 | Integrated: 0.973 Excised: 0.970 |
| Some of the most statistically significant different genes between ES and iPS cells | Primary iPS: GAS1, FGFR4, MSX2 Secondary iPS: RAD51, LEFTY2, MSX2 | GSTM2, DNAJC15, CTNNB1 | iPS: IAH1, RELL2, GNG3 | NPM1, RPL29, NDUFB2 | iPS: ROCK1, EPS15, CITED2 | SLITRK4, ZFP208, CR1 | GLIPR1, SOX11, ELAVL1 | Integrated: PLCL2, LEFTY2Excised: MEG3, ZNF273 |
Summary of the datasets and the reprogramming experiment used for the comparison of ESCs and iPSCs. For each dataset, the correlation coefficient on the percentranks for the genome-wide profile (average and, in parenthesis, minimum and maximum correlation between ES and iPS samples hybridized) is given, as well as for the profile of 316 bivalent-domain containing genes, which reflects more stringently the functional equivalence in terms of the differentiation potential between ESCs and iPSCs. Some of the most significantly differentially expressed genes between ESCs and iPSCs for each dataset are also shown.