Table 2.
Seventy-Six Genes with Decreased 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× | OFF | CLUST |
|---|---|---|---|---|---|---|---|---|---|---|
| 12 | SERPINA3 | serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 | 2 | 25 | 64.0% | 60.0% | 48.0% | 24.0% | 0.0% | 1 |
| 51761 | ATP8A2 | ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2 | 1 | 15 | 60.0% | 53.3% | 40.0% | 26.7% | 0.0% | 1 |
| 51129 | ANGPTL4 | angiopoietin-like 4 | 1 | 18 | 66.7% | 61.1% | 22.2% | 5.6% | 0.0% | 2 |
| 348 | APOE | apolipoprotein E | 2 | 32 | 59.4% | 50.0% | 31.3% | 6.3% | 0.0% | 5 |
| 5004 | ORM1 | orosomucoid 1 | 1 | 19 | 57.9% | 42.1% | 26.3% | 15.8% | 0.0% | 1 |
| 3240 | HP | haptoglobin | 7 | 29 | 51.7% | 41.4% | 27.6% | 17.2% | 0.0% | 1 |
| 6347 | CCL2 | chemokine (C-C motif) ligand 2 | 2 | 21 | 71.4% | 42.9% | 14.3% | 4.8% | 0.0% | 5 |
| 27295 | PDLIM3 | PDZ and LIM domain 3 | 1 | 14 | 64.3% | 50.0% | 7.1% | 0.0% | 7.1% | 5 |
| 213 | ALB | albumin | 1 | 14 | 50.0% | 35.7% | 21.4% | 14.3% | 0.0% | 2 |
| 7076 | TIMP1 | tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) | 3 | 31 | 67.7% | 41.9% | 6.5% | 0.0% | 0.0% | 6 |
| 2335 | FN1 | fibronectin 1 | 4 | 32 | 56.3% | 40.6% | 18.8% | 0.0% | 0.0% | 6 |
| 710 | SERPING1 | serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary) | 1 | 26 | 50.0% | 34.6% | 26.9% | 3.8% | 0.0% | 5 |
| 8553 | BHLHB2 | basic helix-loop-helix domain containing, class B, 2 | 1 | 26 | 57.7% | 53.8% | 0.0% | 0.0% | 0.0% | 6 |
| 3303 | HSPA1A | heat shock 70kDa protein 1A | 4 | 31 | 48.4% | 35.5% | 22.6% | 3.2% | 0.0% | 3 |
| 6373 | CXCL11 | chemokine (C-X-C motif) ligand 11 | 1 | 11 | 63.6% | 18.2% | 9.1% | 0.0% | 18.2% | 5 |
| 56937 | TMEPAI | transmembrane, prostate androgen induced RNA | 1 | 25 | 48.0% | 40.0% | 16.0% | 4.0% | 0.0% | 6 |
| 6035 | RNASE1 | ribonuclease, RNase A family, 1 (pancreatic) | 1 | 29 | 55.2% | 31.0% | 13.8% | 6.9% | 0.0% | 3 |
| 2316 | FLNA | filamin A, alpha (actin binding protein 280) | 2 | 31 | 51.6% | 41.9% | 12.9% | 0.0% | 0.0% | 5 |
| 768 | CA9 | carbonic anhydrase IX | 1 | 18 | 44.4% | 33.3% | 16.7% | 0.0% | 11.1% | 6 |
| 2885 | GRB2 | growth factor receptor-bound protein 2 | 1 | 21 | 57.1% | 33.3% | 14.3% | 0.0% | 0.0% | 5 |
| 7564 | ZNF16 | zinc finger protein 16 (KOX 9) | 1 | 27 | 51.9% | 44.4% | 7.4% | 0.0% | 0.0% | 6 |
| 4070 | TACSTD2 | tumor-associated calcium signal transducer 2 | 1 | 28 | 50.0% | 28.6% | 17.9% | 7.1% | 0.0% | 6 |
| 7052 | TGM2 | transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) | 1 | 28 | 57.1% | 32.1% | 14.3% | 0.0% | 0.0% | 6 |
| 4071 | TM4SF1 | transmembrane 4 superfamily member 1 | 1 | 29 | 51.7% | 41.4% | 6.9% | 3.4% | 0.0% | 4 |
| 10397 | NDRG1 | N-myc downstream regulated gene 1 | 1 | 30 | 56.7% | 40.0% | 6.7% | 0.0% | 0.0% | 2 |
| 2207 | FCER1G | Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide | 1 | 21 | 61.9% | 33.3% | 4.8% | 0.0% | 0.0% | 5 |
| 1152 | CKB | creatine kinase, brain | 3 | 32 | 50.0% | 31.3% | 12.5% | 6.3% | 0.0% | 3 |
| 1514 | CTSL | cathepsin L | 4 | 31 | 54.8% | 29.0% | 9.7% | 3.2% | 0.0% | 5 |
| 652 | BMP4 | bone morphogenetic protein 4 | 1 | 24 | 50.0% | 37.5% | 8.3% | 0.0% | 0.0% | 6 |
| 633 | BGN | biglycan | 1 | 24 | 58.3% | 37.5% | 0.0% | 0.0% | 0.0% | 1 |
| 3936 | LCP1 | lymphocyte cytosolic protein 1 (L-plastin) | 1 | 23 | 47.8% | 26.1% | 13.0% | 8.7% | 0.0% | 5 |
| 2878 | GPX3 | glutathione peroxidase 3 (plasma) | 1 | 18 | 55.6% | 33.3% | 5.6% | 0.0% | 0.0% | 1 |
| 7422 | VEGF | vascular endothelial growth factor | 2 | 30 | 53.3% | 33.3% | 6.7% | 0.0% | 0.0% | 2 |
| 4256 | MGP | matrix Gla protein | 1 | 30 | 46.7% | 36.7% | 10.0% | 0.0% | 0.0% | 1 |
| 374 | AREG | amphiregulin (schwannoma-derived growth factor) | 1 | 29 | 44.8% | 27.6% | 13.8% | 6.9% | 0.0% | 4 |
| 7701 | ZNF142 | zinc finger protein 142 (clone pHZ-49) | 1 | 28 | 46.4% | 32.1% | 14.3% | 0.0% | 0.0% | 3 |
| 51366 | DD5 | progestin induced protein | 1 | 27 | 44.4% | 37.0% | 11.1% | 0.0% | 0.0% | 6 |
| 10457 | GPNMB | glycoprotein (transmembrane) nmb | 1 | 26 | 50.0% | 30.8% | 11.5% | 0.0% | 0.0% | 5 |
| 22822 | PHLDA1 | pleckstrin homology-like domain, family A, member 1 | 1 | 24 | 50.0% | 33.3% | 8.3% | 0.0% | 0.0% | 6 |
| 10123 | ARL7 | ADP-ribosylation factor-like 7 | 3 | 32 | 46.9% | 31.3% | 6.3% | 6.3% | 0.0% | 6 |
| 4316 | MMP7 | matrix metalloproteinase 7 (matrilysin, uterine) | 6 | 32 | 46.9% | 31.3% | 9.4% | 3.1% | 0.0% | 6 |
| 3576 | IL8 | interleukin 8 | 1 | 21 | 47.6% | 33.3% | 4.8% | 4.8% | 0.0% | 6 |
| 5163 | PDK1 | pyruvate dehydrogenase kinase, isoenzyme 1 | 1 | 29 | 58.6% | 31.0% | 0.0% | 0.0% | 0.0% | 2 |
| 1649 | DDIT3 | DNA-damage-inducible transcript 3 | 1 | 28 | 46.4% | 35.7% | 7.1% | 0.0% | 0.0% | 2 |
| 7033 | TFF3 | trefoil factor 3 (intestinal) | 1 | 27 | 44.4% | 22.2% | 14.8% | 3.7% | 3.7% | 3 |
| 4493 | MT1E | metallothionein 1E (functional) | 1 | 26 | 46.2% | 30.8% | 11.5% | 0.0% | 0.0% | 3 |
| 7481 | WNT11 | wingless-type MMTV integration site family, member 11 | 1 | 17 | 52.9% | 23.5% | 5.9% | 0.0% | 5.9% | 4 |
| 10381 | TUBB4 | tubulin, beta, 4 | 1 | 15 | 60.0% | 26.7% | 0.0% | 0.0% | 0.0% | 1 |
| 5270 | SERPINE2 | serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 | 1 | 28 | 46.4% | 32.1% | 3.6% | 3.6% | 0.0% | 6 |
| 9590 | AKAP12 | A kinase (PRKA) anchor protein (gravin) 12 | 1 | 20 | 50.0% | 25.0% | 5.0% | 5.0% | 0.0% | 2 |
| 54206 | MIG-6 | mitogen-inducible gene 6 | 1 | 31 | 45.2% | 35.5% | 3.2% | 0.0% | 0.0% | 2 |
| 11067 | C10orf10 | chromosome 10 open reading frame 10 | 1 | 24 | 62.5% | 20.8% | 0.0% | 0.0% | 0.0% | 6 |
| 2159 | F10 | coagulation factor X | 1 | 18 | 50.0% | 33.3% | 0.0% | 0.0% | 0.0% | 4 |
| 57561 | ARRDC3 | arrestin domain containing 3 | 3 | 27 | 59.3% | 22.2% | 0.0% | 0.0% | 0.0% | 6 |
| 4495 | MT1G | metallothionein 1G | 1 | 27 | 44.4% | 22.2% | 11.1% | 3.7% | 0.0% | 3 |
| 10628 | TXNIP | thioredoxin interacting protein | 5 | 32 | 46.9% | 31.3% | 3.1% | 0.0% | 0.0% | 3 |
| 3939 | LDHA | lactate dehydrogenase A | 2 | 32 | 53.1% | 25.0% | 3.1% | 0.0% | 0.0% | 6 |
| 6890 | TAP1 | transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) | 1 | 24 | 45.8% | 20.8% | 8.3% | 4.2% | 0.0% | 3 |
| 1942 | EFNA1 | ephrin-A1 | 1 | 28 | 46.4% | 32.1% | 0.0% | 0.0% | 0.0% | 4 |
| 136 | ADORA2B | adenosine A2b receptor | 1 | 22 | 50.0% | 27.3% | 0.0% | 0.0% | 0.0% | 3 |
| 11145 | HRASLS3 | HRAS-like suppressor 3 | 1 | 26 | 46.2% | 30.8% | 0.0% | 0.0% | 0.0% | 6 |
| 84951 | CTEN | C-terminal tensin-like | 1 | 21 | 52.4% | 19.0% | 4.8% | 0.0% | 0.0% | 6 |
| 90637 | LOC90637 | hypothetical protein LOC90637 | 1 | 29 | 44.8% | 27.6% | 3.4% | 0.0% | 0.0% | 2 |
| 7045 | TGFBI | transforming growth factor, beta-induced, 68kDa | 1 | 24 | 50.0% | 25.0% | 0.0% | 0.0% | 0.0% | 6 |
| 5230 | PGK1 | phosphoglycerate kinase 1 | 1 | 32 | 46.9% | 25.0% | 3.1% | 0.0% | 0.0% | 6 |
| 64065 | PERP | PERP, TP53 apoptosis effector | 1 | 28 | 46.4% | 17.9% | 3.6% | 3.6% | 0.0% | 6 |
| 9531 | BAG3 | BCL2-associated athanogene 3 | 1 | 28 | 42.9% | 25.0% | 3.6% | 0.0% | 0.0% | 2 |
| 23023 | KIAA0779 | KIAA0779 protein | 1 | 21 | 47.6% | 23.8% | 0.0% | 0.0% | 0.0% | 3 |
| 567 | B2M | beta-2-microglobulin | 1 | 28 | 46.4% | 17.9% | 0.0% | 0.0% | 0.0% | 3 |
| 2317 | FLNB | filamin B, beta (actin binding protein 278) | 1 | 28 | 42.9% | 14.3% | 7.1% | 0.0% | 0.0% | 3 |
| 665 | BNIP3L | BCL2/adenovirus E1B 19kDa interacting protein 3-like | 2 | 30 | 46.7% | 16.7% | 0.0% | 0.0% | 0.0% | 2 |
| 7431 | VIM | vimentin | 1 | 28 | 42.9% | 14.3% | 3.6% | 0.0% | 0.0% | 5 |
| 91452 | ACBD5 | acyl-Coenzyme A binding domain containing 5 | 1 | 27 | 44.4% | 14.8% | 0.0% | 0.0% | 0.0% | 4 |
| 1508 | CTSB | cathepsin B | 1 | 31 | 48.4% | 9.7% | 0.0% | 0.0% | 0.0% | 6 |
| 55818 | JMJD1 | jumonji domain containing 1 | 1 | 28 | 42.9% | 14.3% | 0.0% | 0.0% | 0.0% | 6 |
| 5763 | PTMS | parathymosin | 1 | 31 | 41.9% | 12.9% | 0.0% | 0.0% | 0.0% | 3 |
The columns are the same as in Table 1, except that the prevalence columns indicate percentage of patients exhibiting downregulation and the “OFF” column indicates the percentage of patients where expression was detected in the primary tumor but not the metastasis.