Table 2.
Selected pathway components showing differential expression between VHL and MEN 2 tumors by microarray and/or proteomics analysis
| Gene Symbol | Component | Gene ID |
Microarray |
Proteomics (Δ) | PMID | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P Value | Δ | |||||||||||
| Positive control pathway components | ||||||||||||
| PNMT | Phenylethanolamine N-methyltransferase | 5409 | 0.000* | 11.8 | 300.1 | 11344198 | ||||||
| NPY | Neuropeptide Y | 4852 | 0.001* | 5.3 | 184.1 | 17470513 | ||||||
| CHGB | Chromogranin B | 1114 | 0.002 | 22.9 | 11.5 | 17639059 | ||||||
| SLC6A2 | Sodium-dependent norepinephrine transporter | 6530 | 0.006* | 4.3 | 8.2 | 16189177 | ||||||
| CHGA | Chromogranin A | 1113 | 0.010 | 7.0 | 3.9 | 18046660 | ||||||
| TH | Tyrosine hydroxylase | 7054 | 0.004 | 5.7 | 3.0 | 11344198 | ||||||
| Other selected pathway components | ||||||||||||
| SNAP25 | Synaptosomal-associated protein, 25 kDa† | 6616 | 0.000 | 0.4 | 22.5 | 18064413 | ||||||
| ANXA7 | Annexin A7† | 310 | 0.000 | 3.4 | 12438137 | |||||||
| RPH3A | Rabphilin 3A† | 22895 | 0.000 | 5.6 | 33.0 | 10364266 | ||||||
| CADPS | Ca2+-dependent secretion activator† | 8618 | 0.006* | 5.8 | 10460244 | |||||||
| CALM1 | Calmodulin 1† | 801 | 0.000 | 11.8 | 12145198 | |||||||
| CALM2 | Calmodulin 2† | 805 | 0.000* | 15.8 | 17601619 | |||||||
| SNPH | Syntaphilin† | 9751 | 0.001 | 2.3 | 14985338 | |||||||
| SYT1 | Synaptotagmin I† | 6857 | 0.059 | 0.4 | 43.1 | 18275379 | ||||||
| RAB27B | RAB27B, member RAS oncogene family† | 5874 | 0.006 | 3.1 | 21.4 | 17664848 | ||||||
| SYTL2 | Synaptotagmin-like 2† | 54843 | 0.001 | 5.3 | 11773082 | |||||||
| RAB8B | RAB8B, member RAS oncogene family | 51762 | 0.007 | 2.5 | 3.3 | 11278749 | ||||||
| RAB27A | RAB27A, member RAS oncogene family | 5873 | 0.007 | 1.6 | 61.3 | 17664848 | ||||||
| STX16 | Syntaxin 16 | 8675 | 0.004* | 1.5 | 9.5 | 18337752 | ||||||
| VAT1 | Vesicle amine transport protein 1 homolog | 10493 | 0.000* | 1.7 | 1.8 | 7905859 | ||||||
| ERC2 | ELKS/RAB6-interacting/CAST family member 2 | 26059 | 0.045 | 2.1 | 5.7 | 16421316 | ||||||
| PCSK2 | Proprotein convertase subtilisin/kexin type 2 | 5126 | 0.001 | 5.7 | 56.7 | 15196022 | ||||||
| PCSK1 | Proprotein convertase subtilisin/kexin type 1 | 5122 | 0.038 | 24.6 | 17556096 | |||||||
| SNAPAP | SNAP-associated protein | 23557 | 0.030* | 1.9 | 33.6 | 16280592 | ||||||
| NCAM1 | Neural cell adhesion molecule 1 | 4684 | 0.000 | 2.7 | 47.7 | 15800072 | ||||||
| NAPB | N-ethylmaleimide-sensitive factor attachment protein-β | 63908 | 0.002 | 3.1 | 38.2 | 16795052 | ||||||
| NSF | N-ethylmaleimide-sensitive factor | 4905 | 18.9 | 17080482 | ||||||||
| SCAMP1 | Secretory carrier membrane protein 1 | 9522 | 0.001* | 2.2 | 17355250 | |||||||
| SCAMP3 | Secretory carrier membrane protein 3 | 10067 | 0.003* | 1.7 | 17355250 | |||||||
| EXOC3 | Exocyst complex component 3 | 11336 | 0.001 | 5.0 | 12763070 | |||||||
| SYNGR1 | Synaptogyrin 1 | 9145 | 0.000 | 2.7 | 17355250 | |||||||
| SYTL1 | Synaptotagmin-like 1 | 84958 | 0.001 | 2.1 | 11243866 | |||||||
| RAB3B | RAB3B, member RAS oncogene family | 5865 | 305.0 | 7834495 | ||||||||
| VGF | VGF nerve growth factor inducible | 7425 | 0.868 | 1.1 | 192.0 | 16221685 | ||||||
| VAPA | VAMP-associated protein A | 9218 | 0.376 | 1.2 | 92.7 | 11511104 | ||||||
| VAPB | VAMP-associated protein B | 9217 | 0.353 | 1.3 | 74.4 | 11511104 | ||||||
| VAMP1 | Vesicle-associated membrane protein 1 | 6843 | 0.041 | 1.5 | 76.2 | 17355250 | ||||||
| STX1A | Syntaxin 1A | 6804 | 0.753 | 1.2 | 16.4 | 10369670 | ||||||
| STX1B2 | Syntaxin 1B2† | 112755 | 0.001 | 0.5 | 9200718 | |||||||
| UNC13B | Unc-13 homolog B (C. elegans)† | 10497 | 0.001 | 0.1 | 12893529 | |||||||
| ARHGDIB | Rho GDP dissociation inhibitor (GDI)-β | 397 | 0.000 | 0.3 | 0.01 | 8978674 | ||||||
| SV2A | Synaptic vesicle glycoprotein 2A | 9900 | 0.000 | 0.1 | 16436618 | |||||||
| SCGB3A1 | Secretoglobin, family 3A, member 1 | 92304 | 0.000 | 0.2 | 18194566 | |||||||
| GSN | Gelsolin (amyloidosis, Finnish type) | 2934 | 0.001 | 0.2 | 1.0 | 8388266 | ||||||
| SYT6 | Synaptotagmin VI | 148281 | 0.002 | 0.1 | 7791877 | |||||||
| SNIP | SNAP25-interacting protein | 80725 | 0.000 | 0.1 | 10625663 | |||||||
Values for microarrays indicate levels of significance (P values) and relative directional signals (Δ) of components in multiple endocrine neoplasma type 2 (MEN 2) vs. von Hippel-Lindau (VHL) tumors (for either oligonucleotide or cDNA arrays). PMID, PubMed unique identifiers; VAMP, vesicle-associated membrane protein. Values for the proteomics analysis indicate Δ of components in MEN 2 vs. to VHL tumors. Signals >1 indicate higher expression in MEN 2 than in VHL tumors and <1 lower expression in MEN 2 than VHL tumors. PMID provide confirmatory references either for components with previously established higher expression in MEN 2 than VHL tumors (positive control pathway components) or that support inclusion in the selection as components of secretory pathways.
Component showing significant differences by both cDNA and oligonuclotide arrays;
components selected for followup quantitative PCR.