Table 1.
Top 40 differentially expressed proteins between WERI-RB1 and WERI-ETOR cell lines detected by machine-learning algorithms (LASSO, elastic nets, random forests, extreme gradient boosting). Proteins are sorted according to their fold-change. Log fold-change > 0 represents a higher expression of the protein in the WERI-ETOR group. Significance was calculated using four commonly accepted methods in the literature (Welch t-test, limma, edgeR, DESeq2) and merged (meta.q-value).
| Gene Symbol | Full Protein Name | Chromosome | Meta.q-Value | Log Fold-Change [WERI-ETOR/WERI-RB1] |
|---|---|---|---|---|
| DHRS2 | Dehydrogenase/reductase SDR family member 2 | 14 | 3.051 × 10−5 | 4.062 |
| S100A1 | Protein S100-A1 | 1 | 1.275 × 10−6 | 3.828 |
| KRT8 | Keratin 8 | 12 | 6.307 × 10−4 | 3.762 |
| NTM | NAC domain-containing protein 69 | 11 | 2.402 × 10−4 | 3.368 |
| EPPK1 | Epiplakin | 8 | 1.879 × 10−4 | 2.910 |
| AHNAK | AHNAK nucleoprotein | 11 | 3.570 × 10−4 | 2.708 |
| SEPTIN6 | Septin 6 | X | 1.262 × 10−4 | 2.540 |
| TES | Testin | 7 | 1.615 × 10−5 | 2.513 |
| DIAPH1 | Protein diaphanous homolog 1 | 5 | 3.634 × 10−6 | 2.174 |
| GNPDA1 | Glucosamine-6-phosphate isomerase 1 | 5 | 1.576 × 10−6 | 2.158 |
| CRLF3 | Cytokine receptor like factor 3 | 17 | 5.155 × 10−4 | 1.942 |
| MEX3A | RNA-binding protein MEX3A | 1 | 4.712 × 10−5 | −1.871 |
| CDH2 | Cadherin-2 | 18 | 1.581 × 10−5 | −1.955 |
| TOP2B | DNA topoisomerase 2-beta | 3 | 8.151 × 10−6 | −2.155 |
| CDK6 | Cyclin-dependent kinase 6 | 7 | 7.362 × 10−5 | −2.156 |
| ATP2B1 | Plasma membrane calcium-transporting ATPase 1 | 12 | 7.630 × 10−6 | −2.160 |
| TOP2A | DNA topoisomerase 2-alpha | 17 | 6.932 × 10−7 | −2.178 |
| GNAT2 | Guanine nucleotide-binding protein G(t) subunit alpha-2 | 1 | 2.064 × 10−5 | −2.189 |
| SERPINE2 | Serpin family E member 2 | 2 | 3.716 × 10−4 | −2.201 |
| OCIAD2 | OCIA domain-containing protein 2 | 4 | 2.556 × 10−6 | −2.234 |
| CAMK2D | Calcium-dependent protein kinase II | 4 | 3.350 × 10−5 | −2.238 |
| CTNNBIP1 | Catenin-beta-interacting protein 1 | 1 | 4.668 × 10−3 | −2.408 |
| LMOD1 | Leiomodin-1 | 1 | 6.385 × 10−6 | −2.534 |
| ACBD7 | Acyl-CoA-binding domain-containing protein 7 | 10 | 1.349 × 10−5 | −2.720 |
| GDAP1L1 | Ganglioside-induced differentiation-associated protein 1-like 1 | 20 | 5.081 × 10−5 | −2.734 |
| PLIN2 | Perilipin-2 | 9 | 1.793 × 10−5 | −2.769 |
| DPYSL3 | Dihydropyrimidinase like 3 | 5 | 1.096 × 10−5 | −2.792 |
| AMPH | D-alanyl-D-alanine-carboxypeptidase/endopeptidase AmpH | 7 | 6.121 × 10−6 | −2.842 |
| MAP2 | Microtubule-associated protein 2 | 2 | 3.928 × 10−5 | −2.966 |
| ATP1B1 | Sodium/potassium-transporting ATPase subunit beta-1 | 1 | 2.994 × 10−5 | −3.000 |
| GNGT2 | Guanine nucleotide-binding protein subunit gamma-T2 | 17 | 8.151 × 10−6 | −3.000 |
| CRX | Cone-rod homeobox protein | 19 | 1.636 × 10−4 | −3.177 |
| GAP43 | Neuromodulin | 3 | 3.011 × 10−3 | −3.236 |
| SH3BGRL | SH3 domain-binding glutamic acid-rich-like protein 3 | X | 5.071 × 10−5 | −3.325 |
| TAGLN3 | Transgelin-3 | 3 | 3.634 × 10−6 | −3.346 |
| ACAA2 | 3-ketoacyl-CoA thiolase | 18 | 2.119 × 10−7 | −3.640 |
| BASP1 | Brain-acid-soluble protein 1 | 5 | 1.879 × 10−4 | −3.664 |
| RCVRN | Recoverin | 17 | 2.248 × 10−4 | −3.886 |
| MACROH2A2 | Core histone macro-H2A.2 | 10 | 1.791 × 10−5 | −4.777 |
| H1-5 | Histone H1.5 | 6 | 2.846 × 10−6 | −7.812 |