Table 1.
Functional annotation cluster analysis (DAVID) of iTRAQ expression data
| (a) Differentiated v liver up-regulated | |||
|---|---|---|---|
| Annotation cluster | Count | Enrichment score | p value |
| Actin binding | 65 | 12.11 | 8.22E–13 |
| Cell–cell adhesion | 117 | 9.73 | 7.58E–13 |
| Spliceosome | 54 | 4.07 | 5.60E–10 |
| PI3K-Akt signaling | 44 | 4.02 | 2.18E–05 |
| EF hand domain | 30 | 3.89 | 1.66E–04 |
| SAP domain | 11 | 3.73 | 6.67E–05 |
| LIM domain | 18 | 3.53 | 2.76E–06 |
| SH3 domain | 34 | 3.17 | 1.59E–04 |
| Chromosome | 44 | 3.08 | 1.63E–06 |
| (b) Differentiated v liver down-regulated | |||
|---|---|---|---|
| Annotation cluster | Count | Enrichment score | p value |
| Mitochondrion | 457 | 32.54 | 2.59E–43 |
| Oxidoreductase | 223 | 25.39 | 1.75E–32 |
| Respiratory chain | 45 | 13.48 | 2.74E–19 |
| Fatty acid/lipid metabolism | 107 | 12.32 | 6.16E–13 |
| Ribosomal protein | 83 | 12.06 | 8.54E–15 |
| Peroxisome | 50 | 6.56 | 1.90E–10 |
| Endoplasmic reticulum | 170 | 5.57 | 3.07E–06 |
| Flavoprotein | 48 | 4.84 | 1.13E–07 |
| Proteasome | 35 | 4.37 | 2.98E–10 |
| Cytochrome P450 | 29 | 3.51 | 6.34E–05 |
| Proteolysis | 25 | 3.18 | 2.14E–07 |
| (c) Differentiated v undifferentiated up-regulated | |||
|---|---|---|---|
| Annotation cluster | Count | Enrichment score | p value |
| Oxidoreductase | 90 | 13.09 | 1.07E–13 |
| Mitochondrion | 136 | 11.76 | 3.73E–12 |
| Signal peptide/secreted | 107 | 5.19 | 5.52E–07 |
| Respiratory chain | 23 | 4.04 | 4.86E–04 |
| Amino acid metabolism | 15 | 3.97 | 2.53E–05 |
| Glutathione metabolism | 16 | 3.13 | 4.17E–05 |
| Fatty acid/lipid metabolism | 24 | 3.03 | 9.26E–04 |
| Aldehyde dehydrogenase | 8 | 2.67 | 7.41E–04 |
| Calcium | 42 | 2.30 | 3.21E–05 |
| Cytochrome P450 | 16 | 2.16 | 6.21E–04 |
| Protease inhibitor | 11 | 2.14 | 4.81E–04 |
| (d) Differentiated v undifferentiated down-regulated | |||
|---|---|---|---|
| Annotation cluster | Count | Enrichment score | p value |
| Ribosomal protein | 86 | 38.95 | 4.90E–38 |
| Protein biosynthesis | 61 | 9.24 | 1.39E–24 |
| Chaperone | 47 | 7.73 | 5.43E–11 |
| Proteasome | 39 | 7.64 | 1.59E–24 |
| Ribosomal biogenesis | 23 | 5.89 | 5.51E–08 |
| Aminoacyl-tRNA synthesis | 20 | 2.91 | 1.37E–07 |
| ATPase activity | 24 | 2.79 | 1.74E–04 |
| ATP binding | 110 | 2.40 | 3.61E–04 |
(a) Functions up-regulated in differentiated organoids compared to liver. (b) Functions down-regulated in differentiated organoids compared to liver. (c) Functions up-regulated in differentiated compared to undifferentiated organoids. (d) Functions down-regulated in differentiated compared to undifferentiated organoids