Table 3. Transcriptional profile of genes expressed in (i) UGE, (ii) in both UGE and Sca-1Hi and (iii) Sca-1Hi subsets relative to the Sca-1Neg subset.
| Subset | Category | mRNAs |
| UGE (FPSC) | Cell cycle | Cdc2a (x10) *, E2f3 (x3), Tead2 (x4), Cdc25c (x4), Cdkn3 (x3), Cdk4 (x7), Mcm2 (x5), Mcm6 (x7), Nras (x5), Ccna2 (x9) , Ccne1 (x53), Brca1 (x4), Mki67 (x12) |
| Chromatin modifiers | Ezh2 (x9), Hdac2 (x3), Bmi1 (x2), Jarid1b (x5), Hmga1 (x11), Hmga2 (x47), Suv39h2 (x4), Dnmt3a (x4) | |
| Notch signaling | Lfng (x4), Dll1 (x2) Sdcbp2 (x3) | |
| E2f-target genes | Cdc2a (x10), Cdc6 (x7), Ccne1 (x52), Dhfr (x5), Mcm2 (x4), Mcm5 (x8), Mcm6 (x6), Orc1l (x9), Tk1 (x4), Tyms (x5), Ccna2 (x9)**, Cdca3 (x6)**, Igf2 (x28)**, Mad2l1 (x5)**, Mal2 (x10)**, Rrm2 (x4)**, Tpx2 (x10)**, Ube2c (x5)**, Plk1 (x9)** | |
| Nfy-target genes | Ccnb1 (x12), Ccnb2 (x8), Plk1 (x9), Cdc25c (x2), Ccna2 (x9), Col11a1 (x5), Cdc2a (x10), Hes1 (x2), Tert (x3) | |
| Ap2-target genes | Igf2 (x27), Lor (x28), Cdh1 (x3), Erbb2 (x2) | |
| UGE and Sca-1Hi (FPSC and APSC) | Shh signaling | Shh (x7, x4), Gli3 (x7,NC), Mycn (x82, x2), Hhat (x2, NC), Disp1 (x2, NC), Sufu (x2, NC), Smo (x3, NC), Chek (x8, NC), Ptch1 (x2, NC) |
| Wnt Signaling | Wnt4 (x9, x5), Wnt6 (x8, NC), Fzd6 (x8, x3), Ctnnb1 (x2, NC), Wnt7a (x37, NC), Csnk1g1 (x2, NC), Fzd2 (x3, x-2), Fzd3 (x2, NC), Wnt7b (x4, x2), Wnt9b (x4, NC), Wnt10a (x14, x4), Lrp6 (x2, x3) | |
| Ahr pathway and target genes | Ahr (x4, x5), Tk1 (x5, NC), Syt9 (x17, NC), Cd1d1 (x9, NC), Arnt2 (x5, NC), Smad3 (x5, NC), Magi3 (x4, NC), S100g (x4, NC), Snn (x6, NC), Col11a1 (x5, NC), Mycl1 (x5, NC), Slc2a1 (x5, NC), Lamb3 (x3, x6), Zfp36l1 (x2, x2), Sprr1a (x21, x21), Cdh3 (x5, x2) | |
| ALDH/RA/Retinoid recepror axis | Aldh1a2 (x4, x -7) ***, Rxra (x4, NC), Rarg (x2, x3), Rarb (x6, NC), Crabp2 (x15, NC), Aldh1a3 (x7, x2), Aldh1a7 (x4, x4), Aldh3a1 (x -7, x6), Aldh3b2 (x4, NC) | |
| Epithelial morphogenesis factors | Krt4 (x28, x28), Krt6a (x16, x2), Alcam (x5, x2), Efna5 (x9, x2), Efnb2 (x9, x3), Ephb3 (x7, x3), Celsr1 (x18, x4), Evpl (x10, x4), Ppl (x11, x6) | |
| Phospholipid metabolism | Rxra (x4, NC), Pltp (x2, x8), Akp2 (x2, x2), Lypd2 (x23, x3), Lypd3 (x25, x2), Anxa8 (x8, x6), Lgals3 (x3, x8), Dlk1 (x9, x2), Ly6a (x-2, x18), Tiam1 (x12, x3), Fasn (x2, NC), Hmgcr (x4, NC) | |
| TGFb-pathway and target genes | Clu (x-4, x4), Mmp11 (x8, NC), Smad2 (x2, NC), Smad3 (x3, NC), Lrp1 (x3, x5), Klf4 (x-4, x4), Eng (NC, x4), Junb (x-5, x3), Acvrl1 (NC, x3), Rhoa (NC, x4), Itgfbp3 (NC, x14), Itgb6 (NC, x3) | |
| Detoxification and protection from oxidative stress | Ahr (x4, x5), Aldh1a2 (x4, x -7), Aldh1a3 (x7, x2), Aldh1a7 (x4, x4), Ahr (x4, x5), Cyp2s1 (x2, x4), Cyp2c29 (x2, x3), Cyp51 (x2, NC), Cyp4f39 (x37, NC), Cyp26b1 (NC, x2) | |
| ABC transporters | Abcb1a (x-3, x18 ), Abcd3 (NC, x3), Abcc3 (NC, x3), Abcc4 (x4, x4 ), Abcc5 (NC, x2) | |
| Sca-1Hi (APSC) | Calcium dependent regulators | Thbd (x12), Itpr3 (x2), Anxa3 (x6), S100s10 (x22), Cacna2d4 (x3), Trpc2 (x2), Cbara1 (x6), Ryr2 (-5), Ryr3 (x-3), Itpr2 (x2), |
Functional classification is shown for 146 mRNAs scored as increased relative to differentiated Sca-1Neg cells (Table S3). The average relative increases (fold change) from three comparisons is given in parentheses. When two values are presented in brackets following a gene, the first number represents the fold change in UGE, the second in Sca-1Hi. A mRNA that is present but not increased is denoted NC.
*
Bolded genes represent those that were validated by FACS or qPCR.
**
Specific E2f3-target genes.
***
Aldh activity is elevated in Sca-1Hi cells (Figure 3B).