Table 3.
Lists of Genes Correlated between 2i- and KOSR-Cultured ESCs and Different Stages of Embryonic Development, Related to Figure 2
| Symbols | EPFP | Gene Title | RefSeq |
|---|---|---|---|
| E3.25 versus 2i (z Value, 3.508; Correlation, 0.1001) | |||
| Bhmt2 | 0.0237 | betaine-homocysteine methyltransferase 2 | NM_022884 |
| Spic | 0.0283 | Spi-C transcription factor (Spi-1/PU.1 related) | NM_011461 |
| Jakmip1 | 0.1569 | janus kinase and microtubule interacting protein 1 | NM_178394 |
| Ly6a | 0.2471 | lymphocyte antigen 6 complex, locus A | NM_010738 |
| Gsc | 0.2702 | goosecoid homeobox | NM_010351 |
| Rab38 | 0.2745 | RAB38, member of RAS oncogene family | NM_028238 |
| Khdc1a | 0.2745 | KH domain-containing 1A | NM_183322 |
| Fxyd4 | 0.2859 | FXYD domain-containing ion transport regulator 4 | NM_033648 |
| Bdh1 | 0.319 | 3-hydroxybutyrate dehydrogenase, type 1 | NM_175177 |
| Bcl2l14 | 0.3263 | BCL2-like 14 (apoptosis facilitator) | NM_025778 |
| Cdkn1a | 0.4118 | cyclin-dependent kinase inhibitor 1A (P21) | NM_007669 |
| Gss | 0.4612 | glutathione synthetase | NM_008180 |
| Pdp2 | 0.4887 | pyruvate dehydrogenase phosphatase catalytic subunit 2 | NM_001024606 |
| E3.25 versus KOSR (z Value, 3.59; Correlation, 0.1024) | |||
| Pdgfra | 0.1396 | platelet-derived growth factor receptor, α polypeptide | NM_011058 |
| Cphx1 | 0.3658 | cytoplasmic polyadenylated homeobox 1 | NM_175342 |
| Gata6 | 0.3658 | GATA binding protein 6 | NM_010258 |
| Pnliprp2 | 0.3658 | pancreatic lipase-related protein 2 | NM_011128 |
| E3.5 Epi versus 2i (z Value, 7.351; Correlation, 0.2063) | |||
| Spic | 0.0087 | Spi-C transcription factor (Spi-1/PU.1 related) | NM_011461 |
| Gsc | 0.1293 | goosecoid homeobox | NM_010351 |
| Aspa | 0.1293 | aspartoacylase | NM_023113 |
| Gsta2 | 0.1293 | glutathione S-transferase, α 2 (Yc2) | NM_008182 |
| Mal | 0.3835 | myelin and lymphocyte protein, T cell differentiation protein | NM_010762 |
| Khdc1a | 0.4185 | KH domain-containing 1A | NM_183322 |
| E3.5 PrE versus KOSR (z Value, 7.538; Correlation, 0.2113) | |||
| Pdgfra | 0.1232 | platelet-derived growth factor receptor, α polypeptide | NM_011058 |
| Cubn | 0.1416 | cubilin (intrinsic factor-cobalamin receptor) | NM_001081084 |
| Tcf23 | 0.1416 | transcription factor 23 | NM_053085 |
| Gata4 | 0.236 | GATA binding protein 4 | NM_008092 |
| Cpn1 | 0.236 | carboxypeptidase N, polypeptide 1 | NM_030703 |
| Gata6 | 0.2364 | GATA binding protein 6 | NM_010258 |
| Gdpd5 | 0.2364 | glycerophosphodiester phosphodiesterase domain-containing 5 | NM_201352 |
| Srgn | 0.2364 | serglycin | NM_011157 |
| Meis1 | 0.2364 | Meis homeobox 1 | NM_010789 |
| Sox17 | 0.2364 | SRY (sex determining region Y)-box 17 | NM_011441 |
| Pth1r | 0.2389 | parathyroid hormone 1 receptor | NM_011199 |
| Bmp6 | 0.247 | bone morphogenetic protein 6 | NM_007556 |
| Aqp8 | 0.26 | aquaporin 8 | NM_007474 |
| E4.5 PrE versus KOSR (z Value, 9.405; Correlation, 0.2604) | |||
| Cubn | 0.0421 | cubilin (intrinsic factor-cobalamin receptor) | NM_001081084 |
| Sox7 | 0.3368 | SRY (sex determining region Y)-box 7 | NM_011446 |
| Srgn | 0.3378 | serglycin | NM_011157 |
| Nostrin | 0.3378 | nitric oxide synthase trafficker | NM_181547 |
| Pdgfra | 0.3378 | platelet-derived growth factor receptor, α polypeptide | NM_011058 |
| Sox17 | 0.3439 | SRY (sex determining region Y)-box 17 | NM_011441 |
| Gata4 | 0.3536 | GATA binding protein 4 | NM_008092 |
| Pth1r | 0.3953 | parathyroid hormone 1 receptor | NM_011199 |
| Ctsh | 0.4678 | cathepsin H | NM_007801 |
Pearson correlation of our microarray data of ESCs cultured in serum, 2i, and KOSR and microarrays on different stages of embryonic development (Ohnishi et al., 2014) was determined using ExAtlas online tool for gene expression meta-analysis. The list of correlated genes (FDR ≤0.1, fold change ≥1.5), z value, and correlation value is shown. EPFP, expected proportion of false positives.