TABLE I.
Real-time PCR Validation of Selected Genes in the Microarray Outlier List (Fold Change: −/− vs. +/+) and Putative X-box Sequences in 1kb Mouse Promoters of Validated Genes. Adapted From Zhang et al. (2006)
| GenBank ID | Gene | Gene description | Microarraya | Real-time PCRa | X-box sequences |
|---|---|---|---|---|---|
| Wnt signaling | |||||
| NM_009522 | Wnt3a | Wingless-related MMTV integration site 3A | −2.16 ± 0.10 | −16.17 ± 1.74 | (−) cttgctcttggcaac −640 |
| NM_009521 | Wnt3 | Wingless-related MMTV integration site 3 | −1.99 ± 0.88 | −4.93 ± 0.53 | |
| AK052950 | Fzd10 | Frizzled 10 precusor | −1.56 ± 0.12 | −2.41 ± 0.14 | |
| NM_027280 | Nkd1 | RIKEN cDNA 2810434J10 gene | −1.52 ± 0.03 | −1.98 ± 0.32 | (−) tgtcactcgcaact −715 |
| Retinoic acid signaling | |||||
| NM_007811 | Cyp26a1 | cytochrome P450, 26, retinoic acid | 1.41 ± 0.12 | 1.65 ± 0.20 | (−) tggggcttgcaacc −860
(−) cgggactaggaaca −226 |
| BMP signaling | |||||
| NM_010836 | Msx3 | homeo box, msh-like 3 | −1.89 ± 0.28 | −14.73 ± 1.58 | (−) ggccactagcaact −636 |
| Transcription factors (not in the Wnt, RA, or BMP pathways) | |||||
| NM_031166 | Idb4 | inhibitor of DNA binding 4 | 1.38 ± 0.09 | 1.68 ± 0.22 | (−) ggcgccgggcaacc −470 |
| AK014242 | Fez | RIKEN cDNA 3110069A13 gene | 1.50 ± 0.10 | 1.58 ± 0.10 | |
| NM_013833 | Rax | retina and anterior neural fold homeobox | 1.40 ± 0.05 | 1.90 ± 0.19 | (−) atcgctcttagcaac −899 |
| NM_010446 | Foxa2 | forkhead box A2 | −1.59 ± 0.10 | −1.51 ± 0.09 | (+) gtaaccttgaaaca −123 |
| AK034131 | Rfx4_v3 | regulatory factor X, 4 | −1.32 ± 0.06 | −6.81 ± 2.18 | N/A |
| NM_022435 | Sp5 | trans-acting transcription factor 5 | −2.89 ± 0.19 | −3.76 ± 0.43 | (+) tgtcccgagcaacc −148 |
| AK053799 | Bh1 | homeobox protein B-H1 | −2.68 ± 0.21 | −2.98 ± 0.44 | |
| NM_009573 | Zic1 | zinc finger protein of the cerebellum 1 | −1.85 ± 0.07 | −2.20 ± 0.24 | |
| NM_009575 | Zic3 | zinc finger protein of the cerebellum 3 | −1.63 ± 0.04 | −2.08 ± 0.21 | (−) aatagcaggaaaca −850
(−) gaggctgtggggaac −286 |
| Transmembrane proteins (not in the Wnt, RA, or BMP pathways) | |||||
| NM_010052 | Dlk1 | delta-like homolog | 1.40 ± 0.03 | 1.63 ± 0.10 | |
| NM_008516 | Lrrn1 | leucine rich repeat protein 1, neuronal | −1.79 ± 0.11 | −1.70 ± 0.18 | |
| NM_133241 | Mlc1 | Megalencephalic leukoencephalopathy with subcortical cysts 1 homolog. | −1.63 ± 0.11 | −2.28 ± 0.33 | (−) tatagcaggcaact −965
(+) ggacgctgggaact −418 (+) gctgccatgggaac −15 |
| Cytokines | |||||
| NM_009142 | Cx3cl1 | CX3C ligand 1 | −2.05 ± 0.03 | −2.32 ± 0.12 | (+) tgtttcaggaaact −427
(−) ggcgcgatgggaac −171 (+) ggttccctggcaac −122 |
| Other genes | |||||
| NM_138683 | Rspondin | Mus musculus thrombospondin type 1 | −1.64 ± 0.06 | −1.50 ± 0.25 | (−) agacacctgcaacg −593 |
| NM_011707 | Vtn | vitronectin | −1.46 ± 0.04 | −1.69 ± 0.25 | (+) gggaactaggaact −41 |
| AK044492 | EST | adult retina cDNA, clone: A930016D02 | −2.45 ± 0.22 | −2.78 ± 0.78 | (+) gccccaatggaaac −288 |
a
Mean ± SEM. A negative value indicates decreased expression in −/− vs.+/+, whereas a positive value indicates increased expression. N/A, promoter sequences are not available from the UCSC genome browser. The X-box sequences are identified in either the plus (+) or minus (−) strand, and the positions are shown relative to the transcription start site.