Table 1.
Sixty-Eight Genes with Increased mRNA Expression in Hepatic Metastases Relative to Primary Colon Tumors from the Same Patient
| Locus ID | Symbol | Gene | Spots | N | >1.5× | >2× | >4× | >10× | ON | CLUST |
|---|---|---|---|---|---|---|---|---|---|---|
| 8991 | SELENBP1 | selenium binding protein 1 | 1 | 30 | 56.7% | 43.3% | 23.3% | 6.7% | 0.0% | 3 |
| 163732 | CITED4 | Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4 | 1 | 26 | 53.8% | 38.5% | 23.1% | 7.7% | 0.0% | 3 |
| 4060 | LUM | lumican | 4 | 32 | 62.5% | 43.8% | 15.6% | 0.0% | 0.0% | 5 |
| 5266 | PI3 | protease inhibitor 3, skin-derived (SKALP) | 1 | 26 | 53.8% | 50.0% | 11.5% | 3.8% | 0.0% | 3 |
| 27290 | SPINK4 | serine protease inhibitor, Kazal type 4 | 1 | 21 | 52.4% | 28.6% | 28.6% | 9.5% | 0.0% | 3 |
| 27248 | XTP3TPB | XTP3-transactivated protein B | 1 | 26 | 50.0% | 34.6% | 19.2% | 7.7% | 0.0% | 3 |
| 9518 | GDF15 | growth differentiation factor 15 | 2 | 31 | 51.6% | 38.7% | 16.1% | 3.2% | 0.0% | 6 |
| 374354 | FLJ25621 | FLJ25621 protein | 1 | 23 | 52.2% | 34.8% | 17.4% | 4.3% | 0.0% | 3 |
| 2192 | FBLN1 | fibulin 1 | 2 | 15 | 53.3% | 46.7% | 6.7% | 0.0% | 0.0% | 5 |
| 11167 | FSTL1 | follistatin-like 1 | 2 | 31 | 61.3% | 41.9% | 3.2% | 0.0% | 0.0% | 5 |
| 4313 | MMP2 | matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) | 2 | 26 | 65.4% | 34.6% | 3.8% | 0.0% | 0.0% | 5 |
| 2049 | EPHB3 | EphB3 | 1 | 27 | 48.1% | 33.3% | 18.5% | 3.7% | 0.0% | 6 |
| 800 | CALD1 | caldesmon 1 | 1 | 28 | 50.0% | 39.3% | 10.7% | 3.6% | 0.0% | 5 |
| 57535 | KIAA1324 | maba1 | 1 | 27 | 51.9% | 33.3% | 7.4% | 3.7% | 3.7% | 3 |
| 4535 | MTND1 | NADH dehydrogenase 1 | 2 | 30 | 63.3% | 36.7% | 0.0% | 0.0% | 0.0% | 4 |
| 1634 | DCN | decorin | 6 | 32 | 53.1% | 28.1% | 15.6% | 0.0% | 0.0% | 5 |
| 26073 | POLDIP2 | polymerase (DNA-directed), delta interacting protein 2 | 1 | 27 | 51.9% | 29.6% | 14.8% | 0.0% | 0.0% | 3 |
| 26047 | CNTNAP2 | contactin associated protein-like 2 | 1 | 21 | 52.4% | 28.6% | 4.8% | 0.0% | 9.5% | 4 |
| 1513 | CTSK | cathepsin K (pycnodysostosis) | 1 | 15 | 53.3% | 33.3% | 6.7% | 0.0% | 0.0% | 5 |
| 131177 | FAM3D | family with sequence similarity 3, member D | 1 | 29 | 48.3% | 24.1% | 13.8% | 6.9% | 0.0% | 3 |
| 5786 | PTPRA | protein tyrosine phosphatase, receptor type, A | 1 | 29 | 58.6% | 34.5% | 0.0% | 0.0% | 0.0% | 4 |
| 5327 | PLAT | plasminogen activator, tissue | 2 | 28 | 60.7% | 28.6% | 0.0% | 0.0% | 0.0% | 5 |
| 10406 | WFDC2 | WAP four-disulfide core domain 2 | 1 | 25 | 52.0% | 24.0% | 12.0% | 0.0% | 0.0% | 3 |
| 1278 | COL1A2 | collagen, type I, alpha 2 | 2 | 32 | 43.8% | 31.3% | 9.4% | 3.1% | 0.0% | 5 |
| 132160 | FLJ32332 | likely ortholog of mouse protein phosphatase 2C eta | 1 | 31 | 48.4% | 32.3% | 6.5% | 0.0% | 0.0% | 4 |
| 4536 | MTND2 | NADH dehydrogenase 2 | 2 | 31 | 54.8% | 29.0% | 3.2% | 0.0% | 0.0% | 4 |
| 7433 | VIPR1 | vasoactive intestinal peptide receptor 1 | 1 | 21 | 57.1% | 28.6% | 0.0% | 0.0% | 0.0% | 3 |
| 4091 | MADH6 | MAD, mothers against decapentaplegic homolog 6 (Drosophila) | 1 | 28 | 60.7% | 25.0% | 0.0% | 0.0% | 0.0% | 4 |
| 1277 | COL1A1 | collagen, type I, alpha 1 | 1 | 20 | 50.0% | 30.0% | 5.0% | 0.0% | 0.0% | 5 |
| 1504 | CTRB1 | chymotrypsinogen B1 | 1 | 30 | 53.3% | 26.7% | 3.3% | 0.0% | 0.0% | 4 |
| 6741 | SSB | Sjogren syndrome antigen B (autoantigen La) | 1 | 27 | 55.6% | 25.9% | 0.0% | 0.0% | 0.0% | 4 |
| 27122 | DKK3 | dickkopf homolog 3 (Xenopus laevis) | 1 | 20 | 50.0% | 25.0% | 5.0% | 0.0% | 0.0% | 5 |
| 23469 | PHF3 | PHD finger protein 3 | 1 | 30 | 60.0% | 20.0% | 0.0% | 0.0% | 0.0% | 4 |
| 5908 | RAP1B | RAP1B, member of RAS oncogene family | 1 | 30 | 53.3% | 26.7% | 0.0% | 0.0% | 0.0% | 4 |
| 5295 | PIK3R1 | phosphoinositide-3-kinase, regulatory subunit, polypeptide 1 (p85 alpha) | 1 | 25 | 52.0% | 24.0% | 4.0% | 0.0% | 0.0% | 4 |
| 3297 | HSF1 | heat shock transcription factor 1 | 1 | 30 | 56.7% | 23.3% | 0.0% | 0.0% | 0.0% | 4 |
| 2 | A2M | alpha-2-macroglobulin | 1 | 30 | 46.7% | 26.7% | 6.7% | 0.0% | 0.0% | 5 |
| 81558 | LOC81558 | C/EBP-induced protein | 1 | 29 | 51.7% | 24.1% | 3.4% | 0.0% | 0.0% | 4 |
| 5801 | PTPRR | protein tyrosine phosphatase, receptor type, R | 1 | 29 | 44.8% | 31.0% | 3.4% | 0.0% | 0.0% | 3 |
| 2487 | FRZB | frizzled-related protein | 1 | 18 | 55.6% | 16.7% | 5.6% | 0.0% | 0.0% | 3 |
| 6348 | CCL3 | chemokine (C-C motif) ligand 3 | 1 | 27 | 51.9% | 22.2% | 3.7% | 0.0% | 0.0% | 4 |
| 2006 | ELN | elastin (supravalvular aortic stenosis, Williams-Beuren syndrome) | 1 | 27 | 48.1% | 29.6% | 0.0% | 0.0% | 0.0% | 4 |
| 84859 | MGC4126 | hypothetical protein MGC4126 | 2 | 31 | 45.2% | 25.8% | 6.5% | 0.0% | 0.0% | 5 |
| 4513 | MTCO2 | cytochrome c oxidase II | 3 | 31 | 51.6% | 22.6% | 3.2% | 0.0% | 0.0% | 4 |
| 146880 | MGC40489 | hypothetical protein MGC40489 | 1 | 30 | 46.7% | 26.7% | 3.3% | 0.0% | 0.0% | 4 |
| 83483 | PLVAP | plasmalemma vesicle associated protein | 1 | 25 | 48.0% | 28.0% | 0.0% | 0.0% | 0.0% | 5 |
| 6678 | SPARC | secreted protein, acidic, cysteine-rich (osteonectin) | 1 | 29 | 44.8% | 24.1% | 6.9% | 0.0% | 0.0% | 5 |
| 132241 | LOC132241 | hypothetical protein LOC132241 | 1 | 29 | 51.7% | 20.7% | 3.4% | 0.0% | 0.0% | 4 |
| 67122 | Nrarp | Notch-regulated ankyrin repeat protein | 1 | 28 | 42.9% | 28.6% | 3.6% | 0.0% | 0.0% | 3 |
| 398 | ARHGDIG | Rho GDP dissociation inhibitor (GDI) gamma | 1 | 27 | 44.4% | 18.5% | 11.1% | 0.0% | 0.0% | 4 |
| 51599 | LISCH7 | liver-specific bHLH-Zip transcription factor | 1 | 30 | 50.0% | 23.3% | 0.0% | 0.0% | 0.0% | 4 |
| 81788 | SNARK | likely ortholog of rat SNF1/AMP-activated protein kinase | 1 | 29 | 51.7% | 20.7% | 0.0% | 0.0% | 0.0% | 4 |
| 57605 | PITPNM2 | phosphatidylinositol transfer protein, membrane-associated 2 | 1 | 29 | 51.7% | 20.7% | 0.0% | 0.0% | 0.0% | 4 |
| 51332 | SPTBN5 | spectrin, beta, non-erythrocytic 5 | 1 | 25 | 48.0% | 20.0% | 4.0% | 0.0% | 0.0% | 4 |
| 4541 | MTND6 | NADH dehydrogenase 6 | 6 | 32 | 43.8% | 25.0% | 3.1% | 0.0% | 0.0% | 4 |
| 56940 | DUSP22 | dual specificity phosphatase 22 | 1 | 27 | 48.1% | 22.2% | 0.0% | 0.0% | 0.0% | 5 |
| 2580 | GAK | cyclin G associated kinase | 1 | 27 | 51.9% | 18.5% | 0.0% | 0.0% | 0.0% | 4 |
| 23432 | GPR161 | G protein-coupled receptor 161 | 1 | 29 | 48.3% | 20.7% | 0.0% | 0.0% | 0.0% | 4 |
| 583 | BBS2 | Bardet-Biedl syndrome 2 | 1 | 29 | 48.3% | 20.7% | 0.0% | 0.0% | 0.0% | 4 |
| 2045 | EPHA7 | EphA7 | 1 | 28 | 46.4% | 21.4% | 0.0% | 0.0% | 0.0% | 4 |
| 3189 | HNRPH3 | heterogeneous nuclear ribonucleoprotein H3 (2H9) | 1 | 31 | 48.4% | 19.4% | 0.0% | 0.0% | 0.0% | 4 |
| 1158 | CKM | creatine kinase, muscle | 1 | 30 | 46.7% | 20.0% | 0.0% | 0.0% | 0.0% | 4 |
| 9775 | DDX48 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 48 | 1 | 24 | 45.8% | 20.8% | 0.0% | 0.0% | 0.0% | 4 |
| 10551 | AGR2 | anterior gradient 2 homolog (Xenopus laevis) | 2 | 29 | 41.4% | 24.1% | 0.0% | 0.0% | 0.0% | 3 |
| 1999 | ELF3 | E74-like factor 3 (ets domain transcription factor, epithelial-specific ) | 1 | 30 | 43.3% | 20.0% | 0.0% | 0.0% | 0.0% | 3 |
| 27336 | HTATSF1 | HIV TAT specific factor 1 | 1 | 29 | 44.8% | 17.2% | 0.0% | 0.0% | 0.0% | 4 |
| 7125 | TNNC2 | troponin C2, fast | 1 | 28 | 42.9% | 14.3% | 0.0% | 0.0% | 0.0% | 4 |
| 3040 | HBA2 | hemoglobin, alpha 2 | 1 | 27 | 48.1% | 3.7% | 0.0% | 0.0% | 0.0% | 5 |
Each gene is identified by its LocusLink ID, symbol, and name. The “Spots” column indicates the number of spots (cDNA clones) used to measure each gene’s expression. The “N” column shows the maximum number of patient samples where a particular gene was measured; this number was used in calculating the average percent prevalence across patients. The average prevalence, for cuts of 1.5-, 2-, 4-, and 10- fold increased M/T expression, or cases where the gene was only detected in the metastatic tumor sample (“ON”), is shown as a percentage of the patients where the gene was measured. The “CLUST” column indicates which of the clusters shown in Figure 1 each gene belongs to. The genes are ordered by the sum of the prevalence values, in decreasing order.