Table 3.

Differentially expressed genes initially identified by comparing wild-type and HoxDDel1-13 E12.5 distal forelimb buds

Gene symbol (synonym)Affymetrix probe set IDFold change (FC) microarrayn/91° sample FC by RT-PCR2° sample FC by RT-PCR at E12.5Most significant FC in genitals by RT-PCR
Genes with lower expression in HoxDDel1-13 -mutant forelimbs
Papss2 96713_at1.79±0.72*71.63±0.571.51±0.17**1.83±0.35 at E14.5**
Aldh1a2 (Raldh2) 101707_at1.66±0.33*71.71±0.28**1.54±0.15**None
Stra6 102258_at1.66±0.4741.52±0.531.56±0.34*None
Nr2f1 (Coup-TF1) 102715_at1.56±0.20**71.54±0.12**1.56±0.20**−2.02±0.35 at E14.5**
Gdf10 160860_at1.43±0.4671.55±0.571.79±0.24**2.66±0.76 at E12.5**
Foxp1 96183_at1.44±0.22*61.64±0.32**1.43±0.31None
Lisch7 99452_at1.41±0.16**61.42±0.05**1.20±0.171.25±0.07 at E13.5**
Genes with higher expression in HoxDDel1-13 -mutant forelimbs
Epha3 (Mek4) 95298_at2.06±0.34**91.73±0.43*1.55±0.22**1.75±0.12 at E13.5**
Odz4 98313_at1.80±1.0161.46±0.301.65±0.26**1.47±0.24 at E14.5**
Shox2 (Og12x) 99042_s_at1.62±0.5071.44±0.541.59±0.48*1.33±0.20 at E13.5*
Pcdha (Cnr 1-8) 160610_at1.61±0.32*71.57±0.31*1.62±0.40*−1.29±0.05 at E13.5**
  • All values are the means of three replicates ±s.d.

    *Paired Student's t-test P<0.05; **P-value<0.01.

    n/9, RT-PCR, 1°, 2° samples as in Table 1.

    −FC, change in opposite direction from microarray.

  • This probe set is specific for the constant portion of the Pcdha gene cluster (Sugino et al., 2000), so all isoforms of Pcdha should be detected.

  • The differential expression of Lisch7 was less than 1.4-fold in these secondary samples, but it was maintained on the list because it was significantly different at both E13.5 and E14.5.