Table 3.
Functions predicted for selected genes from 333 DEGs shared by five mouse–prion combinations
| Category | Gene symbola | Description | Entrez ID | Previous studiesb | Human orthologsc |
|---|---|---|---|---|---|
| Protection against oxidative stress | Naprt1* | Nicotinate phosphoribosyltransferase domain containing 1 | 223646 | NAPRT1 | |
| Arachidonate/phospholipid metabolism | Bmp2k* | BMP2-inducible kinase | 140780 | BMP2K | |
| E030018N11Rik* | RIKEN cDNA E030018N11 gene | 319622 | ITPRIPL2 | ||
| Hematopoiesis | Pbxip1* | Pre-B-cell leukemia transcription factor interacting protein 1 | 229534 | PBXIP1 | |
| Chondrogenesis | Loh11cr2a* | Loss of heterozygosity, 11, chromosomal region 2, gene A homolog (human) | 67776 | VWA5A | |
| Complement system (coagulation) | Pp11r* | Placental protein 11 related | 19011 | P11 | |
| BC032204 | cDNA sequence BC032204 | 108101 | X, X4 | FERMT3 | |
| Interferon-related | Aldh1l2* | Aldehyde dehydrogenase 1 family, member L2 | 216188 | ALDH1L2 | |
| D12Ertd647e* | DNA segment, Chr 12, ERATO Doi 647, expressed | 52668 | NA | ||
| Plscr2* | Phospholipid scramblase 2 | 18828 | PLSCR2 | ||
| Other immune response genes | 4632428N05Rik* | RIKEN cDNA 4632428N05 gene | 74048 | C10orf54 | |
| Stno* | Strawberry notch homolog (Drosophila) | 216161 | SBNO2 | ||
| Gp49a | Glycoprotein 49 A | 14727 | X, R | NA | |
| Metal ion binding | Antxr1* | Anthrax toxin receptor 1 | 69538 | ANTXR1 | |
| Dtx3l* | Deltex 3-like (Drosophila) | 209200 | DTX3L | ||
| Eya4* | Eyes absent 4 homolog (Drosophila) | 14051 | EYA4 | ||
| Membrane trafficking | Crispld2* | Cysteine-rich secretory protein LCCL domain containing 2 | 78892 | CRISPLD2 | |
| Signal transduction | 4933428I03Rik* | RIKEN cDNA 4933428I03 gene | 66775 | PTPLAD2 | |
| Nucleic acid binding | Scrg1 | Scrapie responsive gene 1 | 20284 | DD | SCRG1 |
| DNA damage repair | Parp12* | Poly (ADP-ribose) polymerase family, member 12 | 243771 | PARP12 | |
| Guanylate binding | Mpa2l* | Macrophage activation 2 like | 100702 | NA | |
| Neurological disorder related | 0610011I04Rik* | RIKEN cDNA 0610011I04 gene | 66058 | TMEM176A | |
| 1810009M01Rik* | RIKEN cDNA 1810009M01 gene | 65963 | TMEM176B | ||
| Phyhd1* | Phytanoyl-CoA dioxygenase domain containing 1 | 227696 | PHYHD1 | ||
| Non-coding genes | AU020206 | Expressed sequence AU020206 | 101757 | X4 | NA |
| 2310033F14Rik* | RIKEN cDNA 2310033F14 gene | 69555 | NA | ||
| No predicted functions | 1810059G22Rik* | RIKEN cDNA 1810059G22 gene | 67706 | TMEM179B | |
| 2310014H01Rik* | RIKEN cDNA 2310014H01 gene | 76448 | KIAA1949 | ||
| 4933411K20Rik* | RIKEN cDNA 4933411K20 gene | 66756 | KIAA1430 | ||
| 9230105E10Rik* | RIKEN full-length enriched library, clone: A130050C20 product | 245575 | NA | ||
| A530050D06Rik* | RIKEN cDNA A530050D06 gene | 104816 | LOC374569 | ||
| AI452102* | Expressed sequence AI452102 | 330594 | NA | ||
| E230029C05Rik* | RIKEN cDNA E230029C05 gene | 319711 | NA | ||
| 2810459M11Rik | RIKEN cDNA 2810459M11 gene | 72792 | X | C2orf72 | |
| BC025600 | cDNA sequence BC025600 | 231633 | X, Sk | TMEM119 | |
| X99384 | cDNA sequence X99384 | 27355 | X | KIAA1274 | |
| Old gene symbolsd | Updated gene symbol | Description | Entrez ID | Comments | |
| 0610011I04Rik | Tmem176a | Transmembrane protein 176A | 66058 | ||
| 1810009M01Rik | Tmem176b | Transmembrane protein 176B | 65963 | ||
| 1810059G22Rik | Tmem179b | Transmembrane protein 179B | 67706 | ||
| 4933428I03Rik | Ptplad2 | Protein tyrosine phosphatase-like A domain containing 2 | 66775 | ||
| AI452102 | E230029C05Rik | RIKEN cDNA E230029C05 gene | 330594 | New GeneID: 319711 | |
| BC025600 | Tmem119 | Transmembrane protein 119 | 231633 | ||
| BC032204 | Fermt3 | Fermitin family homolog 3 | 108101 | ||
| Cklfsf6 | Cmtm6 | CKLF-like MARVEL transmembrane domain containing 6 | 67213 | ||
| Loh11cr2a | Vwa5a | von Willebrand factor A domain containing 5A | 67776 | ||
| Stno | Sbno2 | Strawberry notch homolog 2 | 216161 |
aGenes with asterisk are unique DEGs to this study; gene in bold and italic shows decreased expression in infected mouse brains.
bX (Xiang et al, 2007); Sk (Skinner et al, 2006); R (Riemer et al, 2004); X4 (Xiang et al, 2004); DD (Dandoy-Dron et al, 1998).
cOrthologous human gene symbols are current as of 28 August 2008. Those denoted as ‘NA' do not have official orthologous human genes.
dGene symbols of the following 10 genes have been updated in the EntrezGene database as of 28 August 2008.