Table I. Potential biomarker candidates chosen for verification by immunohistochemistry.
The adjusted p values for paired Student's t test (two-sided) and fold changes are given. All p values shown are corrected for multiple testing, controlling the false discovery rate. In Progenesis, p values are obtained using the method of Benjamini and Hochberg (21); DeCyder uses the version Benjamini and Hochberg published in 2000 (52). In the case of two values for t test and fold change for one protein, this corresponds to different isoforms identified by 2D-DIGE.
| Number | Protein |
2D-DIGE |
Label-free proteomics |
||||
|---|---|---|---|---|---|---|---|
| Accession | Protein name | Gene name | Paired t test | Fold change | Paired t test | Fold change | |
| Up-regulated in CCC | |||||||
| 1 | P06727 | Apolipoprotein A-IV | APOA4 | 0.010 | 2.3 | 0.003 | 3.9 |
| 2 | O00299 | Chloride intracellular channel protein 1 | CLIC1 | 0.009 | 4.7 | 0.007 | 2.4 |
| 3 | P06396 | Gelsolin | GSN | 0.044 | 5.8 | 0.001 | 5.7 |
| 4 | P26038 | Moesin | MSN | 0.021 | 2.5 | – | – |
| 5 | P14618 | Pyruvate kinase isozymes M1/M2 | PKM2 | 0.025/0.047 | 8.8/2.6 | <0.001 | 7.3 |
| 6 | Q15181 | Inorganic pyrophosphatase | PPA1 | 0.001/0.011 | 2.1/1.8 | – | – |
| 7 | P50454 | Serpin H1 | SERPINH1 | – | – | 0.001 | 3.6 |
| 8 | P31947 | 14-3-3 protein σ | SFN | – | – | 0.01 | 8.2 |
| 9 | P31948 | Stress-induced phosphoprotein 1 | STIP1 | 0.006 | 1.7 | 0.007 | 1.7 |
| Down-regulated in CCC | |||||||
| 10 | P80404 | 4-aminobutyrate aminotransferase, mitochondrial | ABAT | 0.001 | 5.4 | <0.001 | 9.9 |
| 11 | P42765 | 3-ketoacyl-CoA thiolase, mitochondrial | ACAA2 | 0.001/0.001 | 11.7/8.0 | <0.001 | 8.7 |
| 12 | Q93088 | Betaine-homocysteine S-methyltransferase 1 | BHMT | 0.001/0.009 | 11.9/3.1 | <0.001 | 17.1 |
| 13 | P07148 | Fatty acid–binding protein, liver | FABP1 | 0.001 | 30.5 | <0.001 | 22.9 |
| 14 | P54868 | Hydroxymethylglutaryl-CoA synthase, mitochondrial | HMGCS2 | 0.016/0.032 | 2.7/1.8 | <0.001 | 14.0 |