Comparison of cDNA Array, 60-mer Oligo Array, and Q-PCR Relative Expression Results for Placenta-Specific Transcripts
| Putative ID | cDNA array | 60-mer oligo array | Q-PCR | |||||
| Clone name | Ratio | Log(R) | Clone name | Ratio | Log(R) | Ratio | Log(R) | |
| Endocrine-related proteins | ||||||||
| secretin (Sct) | H3001A02 | 199.13 | 2.30 | H3001A02 | 20.94 | 1.32 | 1133.23 | 3.05 |
| placental lactogen II (Csh2) | H3046B04 | 329.47 | 2.52 | J0076G09 | 11.98 | 1.08 | <2965.51 | 3.47 |
| calcyclin (S100a6) | H3087H09 | 35.44 | 1.55 | J0721D01 | 41.17 | 1.61 | 89.74 | 1.95 |
| prolactin-like protein A (Pripa) | H3007C10 | 8.73 | 0.94 | C0102C12 | 9.71 | 0.99 | >366.27 | 2.56 |
| prolactin-like protein M (Pripm) | H3018B06 | 15.87 | 1.20 | C0179D05 | 58.47 | 1.77 | 2680.11 | 3.43 |
| proliferin-related protein (PRP) homolog | H3021D07 | 15.04 | 1.18 | C0191E03 | 59.68 | 1.78 | >4083.91 | 3.61 |
| cathepsin L (Ctsl) | H3028F04 | 3.30 | 0.52 | G0111D11 | 6.58 | 0.82 | 7.09 | 0.85 |
| similar to human nuclear VCP-like protein NVLp.2 | H3076C01 | 13.35 | 1.13 | H3076C01 | 1.23 | 0.09 | ||
| mammary-derived growth inhibitor (Fabp3) | H3104D07 | 47.27 | 1.67 | H3104D07 | 3.05 | 0.48 | 7.34 | 0.87 |
| similar to human HEM45 (Isg20) | H3108A01 | 27.43 | 1.44 | H3108A01 | 1.35 | 0.13 | ||
| Epithelial proteins | ||||||||
| EndoA cytokeratin | H3031C01 | 35.46 | 1.55 | H3031C01 | 31.5 | 1.5 | 81.77 | 1.91 |
| EndoB cytokeratin | H3104F03 | 19.74 | 1.30 | H3104F03 | 20.38 | 1.31 | 75.67 | 1.88 |
| band 3-related protein (Slc4a2) | H3137D09 | 26.46 | 1.42 | H3137D09 | 2.61 | 0.42 | 3.50 | 0.54 |
| similar to tazarotene-induced gene 2 (TIG2) | H3137E09 | 83.09 | 1.92 | H3137E09 | 20.5 | 1.31 | 255.90 | 2.41 |
| basic transcription element binding protein 2 (Bteb2) | H3102C04 | 2.91 | 0.46 | H3102C04 | 1.43 | 0.15 | ||
| Oxidative-, stress-, and aging-related proteins | ||||||||
| 25 kDa mammalian stress protein | H3082D09 | 17.57 | 1.24 | H3082D09 | 12.52 | 1.1 | 25.06 | 1.40 |
| carbonic anhydrase IV (Car4) | H3095H12 | 50055.96 | 4.70 | H3095H12 | 10.31 | 1.01 | 249.37 | 2.40 |
| plasma glutathione peroxidase 3 (Gpx3) | H3125A09 | 40.67 | 1.61 | L0067D11 | 3.1 | 0.49 | 38.54 | 1.59 |
| Cell adhesion- or invasion-related proteins | ||||||||
| Ctla-2-beta, proregion of cysteine protease | H3022D05 | 25.00 | 1.40 | H3022D05 | 53.89 | 1.73 | 240.48 | 2.38 |
| fat facets homolog (Fam)/Usp9x | H3149H05 | 1.44 | 0.16 | L0272F03 | 2.27 | 0.36 | 1.20 | 0.08 |
| annexin XI (Anx11) | H3014B09 | 11.77 | 1.07 | H3014B09 | 8.9 | 0.95 | 53.87 | 1.73 |
| transglutaminase (Tgase) | H3137C06 | 13.29 | 1.12 | H3137C06 | 6.08 | 0.78 | 24.62 | 1.39 |
| ligatin (Lgtn) | H3138F09 | 2.96 | 0.47 | L0236F05 | 1.57 | 0.2 | 1.48 | 0.17 |
| Homeobox and transcription-related proteins | ||||||||
| eHAND (Hand1) | H3020C07 | 4.93 | 0.69 | H3020C07 | 3.88 | 0.59 | 116.49 | 2.07 |
| placenta and embryonic expression gene (Pem) | H3027G05 | 33.28 | 1.52 | G0109E12 | 41.43 | 1.62 | 499.07 | 2.70 |
| placenta-specific homeobox 1 (Psx1) | H3120B02 | 11.88 | 1.07 | L0042E08 | 43.08 | 1.63 | 30.52 | 1.48 |
| cellular repressor of E1A-stimulated genes (Creg) | H3037D10 | 49.63 | 1.70 | J0034A07 | 34.25 | 1.53 | 47.21 | 1.67 |
| melanocyte-specific gene (Msg1) | H3076B01 | 16.42 | 1.22 | H3076B01 | 3.03 | 0.48 | 29.21 | 1.47 |
| transcriptional repressor SIN3B (Sin3B) | H3129D02 | 18.00 | 1.26 | H3129D02 | 11.76 | 1.07 | 12.23 | 1.09 |
| similar to rat Frag1 | H3036E12 | 7.66 | 0.88 | J0029C02 | 0.97 | −0.01 | ||
| Tbx1 | H3051H03 | 2.47 | 0.39 | H3108B10 | 1.86 | 0.27 | 6.57 | 0.82 |
| similar to rat Hbp1 | H3054G12 | 2045.88 | 3.31 | K0136F09 | 1.26 | 0.1 | 1.24 | 0.09 |
| Others expressed in placenta | ||||||||
| LPS-binding protein (Lbp) | H3086G08 | 14.88 | 1.17 | H3086G08 | 2.33 | 0.37 | >3.12 | 0.49 |
| pyruvate carboxylase (Pcx) | H3137A09 | 26.42 | 1.42 | H3137A09 | 1.08 | 0.03 | ||
| Newly defined genes | ||||||||
| protein kinase inhibitor p58 | H3094A04 | 10.09 | 1.00 | H3094A04 | 6.74 | 0.83 | 5.60 | 0.75 |
| similar to human unknown protein IT1 | H3137F09 | 33.60 | 1.53 | L0233B10 | 0.88 | −0.05 | ||
| uroporphyrinogen III synthase (Uros) | H3137F11 | 19.87 | 1.30 | H3137F11 | 1.06 | 0.02 | ||
| Unknown transcripts | ||||||||
| H3005D09 | 11.24 | 1.05 | H3005D09 | 3.73 | 0.57 | 65.10 | 1.81 | |
| H3009D03 | 14.64 | 1.17 | H3009D03 | 39.45 | 1.6 | |||
| H3016D10 | 13.44 | 1.13 | C0172H02 | 50.19 | 1.7 | 341.71 | 2.53 | |
| H3046B06 | 12.66 | 1.10 | J0076H03 | 0.98 | −0.009 | |||
| H3049B11 | 13.32 | 1.12 | H3049B11 | 2.27 | 0.36 | 2.41 | 0.38 | |
| H3050F11 | 7116.94 | 3.85 | H3050F11 | 1.25 | 0.1 | |||
| H3087H10 | 17.02 | 1.23 | H3087H10 | 1.14 | 0.06 | |||
| H3101H01 | 16.32 | 1.21 | H3101H01 | 0.97 | −0.01 | |||
| H3137A10 | 11.82 | 1.07 | H3137A10 | 1.22 | 0.09 | |||
| H3137C08 | 28.54 | 1.46 | L0231F10 | 0.45 | −0.34 | 2.18 | 0.34 | |
| H3137E08 | 95.10 | 1.98 | H3137E08 | 0.93 | −0.03 | |||
| H3137F10 | 10.24 | 1.01 | L0233B11 | 0.58 | −0.24 | 0.37 | −0.44 | |
[i] cDNA microarray data for a set of transcripts previously reported as placenta-specific (modified here from Tanaka et al. 2000) were compared to oligo microarray and Q-PCR expression data. Only those 49 transcripts from the original list which are represented on the NIA 15K cDNA microarray by a sequence-verified clone (the clone set has been sequence-verified since the publication of Tanaka et al. 2000), and on the 60-mer oligo microarray by a BLAST-verified oligo probe, are shown. Of the 71 transcripts validated by Q-PCR, 35 overlap with this list, and this Q-PCR data is included here for comparison. See Supplementary Table 1 for Q-PCR data on all 71 transcripts. Expression ratios are expressed as placenta:embryo, and nonsignificant results are italicized.