Table 2.
Novel intramodular hubs which are differentially expressed across different IPF stages (GSE124685 [25]). Estimates of log2 fold changes (≥0.6 log FC or ≤−0.6 log FC; adjusted p-value < 0.05) in each stage are listed for each candidate gene (see Supplementary Table S7 for additional details).
| Hub Gene | Name | IPF1—Early logFC | IPF2—Progressive logFC | IPF3—Advanced logFC |
|---|---|---|---|---|
| Brown Module | ||||
| CDH3 | Cadherin 3 | 2.16 | 2.53 | 2.59 |
| CFI | Complement factor I | 1.01 | 0.7 | 0.95 |
| CHRDL2 | Chordin like 2 | 1.03 | 2.04 | 1.8 |
| COL10A1 | Collagen type X alpha 1 chain | 2.78 | 2.84 | 2.91 |
| CRABP2 | Cellular retinoic acid binding protein 2 | 2.45 | 3 | 3.25 |
| DCLK1 | Doublecortin-like kinase 1 | 0.86 | 0.94 | 1.04 |
| DOK5 | Docking protein 5 | 1.16 | 1.37 | 1.23 |
| FNDC4 | Fibronectin type III domain containing 4 | 1.04 | 1.19 | 1.29 |
| GPX8 | Glutathione peroxidase 8 (putative) | 1.08 | 0.98 | 1.16 |
| SCRG1 | Stimulator of chondrogenesis 1 | 1.23 | 1.29 | 1.48 |
| SPRR1A | Small proline rich protein 1A | 2.51 | 3.19 | 3.66 |
| STEAP1 | STEAP family member 1 | 1.3 | 1.57 | 1.74 |
| STEAP2 | STEAP2 metalloreductase | 1.03 | 1.35 | 1.34 |
| TDO2 | Tryptophan 2,3-dioxygenase | 2.34 | 2.92 | 2.8 |
| Blue Module | ||||
| AATK | Apoptosis associated tyrosine kinase | −0.94 | −0.96 | −0.99 |
| AFF3 | AF4/FMR2 family member 3 | −1.22 | −1.43 | −1.44 |
| ARHGEF26 | Rho guanine nucleotide exchange factor 26 | −0.91 | −1.14 | −1.27 |
| BTNL9 | Butyrophilin like 9 | −3.39 | −4 | −3.69 |
| C1orf115 | Chromosome 1 open reading frame 115 | −0.85 | −1.14 | −1.26 |
| CDH13 | Cadherin 13 | −0.69 | −0.84 | −0.88 |
| CRTAC1 | Cartilage acidic protein 1 | −1.57 | −2 | −2.33 |
| DENND3 | DENN domain containing 3 | −1.17 | −1.16 | −1.33 |
| EMP2 | Epithelial membrane protein 2 | −0.74 | −1.4 | −1.53 |
| EPB41L5 | Erythrocyte membrane protein band 4.1 like 5 | −0.81 | −1.04 | −1.1 |
| GALNT18 | Polypeptide N-acetylgalactosaminyltransferase 18 | −1.33 | −1.6 | −1.71 |
| GRIA1 | Glutamate ionotropic receptor AMPA type subunit 1 | −0.71 | −1.1 | −1.09 |
| HPCAL1 | Hippocalcin like 1 | −0.86 | −1.34 | −1.71 |
| ITLN2 | Intelectin 2 | −2.29 | −3.52 | −4.18 |
| KANK3 | KN motif and ankyrin repeat domains 3 | −0.92 | −1.08 | −1.16 |
| KCNMB4 | Potassium calcium-activated channel subfamily M regulatory beta subunit 4 | −1.02 | −1.36 | −1.41 |
| MATN3 | Matrilin 3 | −0.92 | −1.4 | −1.61 |
| MYRF | Myelin regulatory factor | −1.43 | −1.59 | −2.13 |
| NDRG4 | NDRG family member 4 | −1.59 | −2.24 | −2.61 |
| NPR1 | Natriuretic peptide receptor 1 | −0.79 | −1.22 | −1.27 |
| OLFML2A | Olfactomedin like 2A | −0.85 | −0.94 | −0.9 |
| PAPSS2 | 3′-phosphoadenosine 5′-phosphosulfate synthase 2 | −0.66 | −1.01 | −1.3 |
| PLLP | Plasmolipin | −0.86 | −1.49 | −1.7 |
| RNF144B | Ring finger protein 144B | −0.65 | −0.91 | −1.17 |
| RS1 | Retinoschisin 1 | −0.71 | −1.61 | −1.79 |
| SERTM1 | Serine rich and transmembrane domain containing 1 | −1.11 | −1.8 | −2.02 |
| STARD8 | StAR related lipid transfer domain containing 8 | −0.95 | −1.08 | −1.29 |
| STXBP6 | Syntaxin binding protein 6 | −0.76 | −1.71 | −2.17 |
| VIPR1 | Vasoactive intestinal peptide receptor 1 | −1.51 | −2.41 | −2.72 |
| VSIG10 | V-set and immunoglobulin domain containing 10 | −0.75 | −1.09 | −0.96 |