Table 2. Selected significantly regulated GO-BPs as well as KEGG pathways in KD 12-day EBs versus Scr 12-day EBs.
| Term | Transcripts | P-value |
|---|---|---|
| Cluster 1: GOs including genes indicated a high expression level in the WT, Scr and KD ESCs and in KD 12-day EBs but with a low expression level in the WT and Scr 12-day EBs | ||
| GO:0034660∼ncRNA metabolic process | 74 | 1.95E−20 |
| GO:0034470∼ncRNA processing | 62 | 6.29E−19 |
| GO:0006396∼RNA processing | 109 | 2.77E−15 |
| GO:0043414∼biopolymer methylation | 25 | 5.71E−07 |
| GO:0040029∼regulation of gene expression, epigenetic | 22 | 2.35E−05 |
| GO:0019827∼stem cell maintenance | 11 | 6.81E−05 |
| Cluster 2: GOs including genes upregulated in the KD 12-day EBs as compared with the WT, Scr and 12-day EBs | ||
| GO:0016125∼sterol metabolic process | 17 | 8.87E−08 |
| GO:0006749∼glutathione metabolic process | 7 | 3.66E−04 |
| GO:0001568∼blood vessel development | 23 | 5.78E−04 |
| GO:0006631∼fatty acid metabolic process | 19 | 7.00E−04 |
| mmu00100:Steroid biosynthesis | 6 | 6.18E−04 |
| mmu00052:Galactose metabolism | 7 | 8.99E−04 |
| mmu03320:PPAR signaling pathway | 11 | 0.002151043 |
| mmu00051:Fructose and mannose metabolism | 7 | 0.004894936 |
| Cluster 3: GOs including genes with low expression levels in WT, Scr and KD ESCs and also in KD 12-day EBs as compared with WT and Scr 12-day EBs | ||
| GO:0007507∼heart development | 79 | 1.70E−18 |
| GO:0001568∼blood vessel development | 74 | 3.02E−13 |
| GO:0060537∼muscle tissue development | 48 | 2.20E−11 |
| GO:0048732∼gland development | 59 | 1.71E−10 |
| GO:0001822∼kidney development | 40 | 1.82E−10 |
| GO:0060348∼bone development | 42 | 3.45E−10 |
| GO:0051216∼cartilage development | 32 | 1.14E−09 |
| GO:0048706∼embryonic skeletal system development | 33 | 1.52E−09 |
| GO:0007420∼brain development | 71 | 2.16E−08 |
| GO:0007417∼central nervous system development | 83 | 9.98E−08 |
| GO:0022008∼neurogenesis | 107 | 8.16E−07 |
| GO:0030324∼lung development | 34 | 1.14E−06 |
| GO:0016055∼Wnt receptor signaling pathway | 37 | 2.45E−06 |
| GO:0017015∼regulation of transforming growth factor-β receptor signaling pathway | 14 | 2.69E−05 |
| Cluster 4: GOs including upregulated in all 12-day EBs populations in comparison with the undifferentiated ESCs populations | ||
| GO:0001568∼blood vessel development | 30 | 2.17E−05 |
| GO:0001944∼vasculature development | 30 | 3.42E−05 |
| GO:0009966∼regulation of signal transduction | 57 | 1.41E−04 |
| GO:0019220∼regulation of phosphate metabolic process | 32 | 1.76E−04 |
| GO:0045597∼positive regulation of cell differentiation | 22 | 2.54E−04 |
| GO:0030324∼lung development | 14 | 0.00450939 |
| GO:0001822∼kidney development | 13 | 0.0087518 |
| GO:0048666∼neuron development | 25 | 0.01569382 |
| GO:0022008∼neurogenesis | 40 | 0.0181755 |
| Cluster 5: GOs including slightly downregulated genes in the KD 12-day EBs as compared with WT and Scr 12-day EBs | ||
| GO:0007507∼heart development | 18 | 2.02E−04 |
| GO:0022008∼neurogenesis | 30 | 6.40E−04 |
| mmu04010:MAPK signaling pathway | 18 | 8.45E−04 |
GOs include genes that are at least twofold up- or downregulated