<p>A) RNA from three sets of triplicate cultures (passage 3 wild type [P3], passage 5 wild type [P5], and passage 3 <i>Tgif1</i> null MEFs [null]) and was analyzed on Affymetrix expression arrays. A Venn diagram is shown with the numbers of probe-sets that changed significantly in each of three pair-wise comparisons (null – P3, null – P5, and P5 – P3). B) An analysis of the overlap between the null – P3 and null – P5 comparisons is shown as a four-way Venn diagram, allowing overlaps between a maximum of two data-sets. The arrows indicate the direction of the change in signal: For example, pale blue arrow indicates increased signal in the null – P3 comparison. Of the 376 probe-sets that increased in the null – P3 comparison, 176 increased and 50 decreased in the null – P5 comparison, whereas 150 did not change significantly in the null – P5. The distribution of changes in the probe-sets present in the overlaps (176, 25, 50, 140) was analyzed using a 2×2 contingency table and a chi squared test. The chi squared value and p-value are shown above. C) An analysis of overlap of the data from the null – P3 and P5 – P3 comparisons is shown, as in panel B. D) Expression of ten genes from the overlaps shown in B and C was analyzed by qRT-PCR in RNAs from triplicate cultures of wild type and <i>Tgif1</i> null MEFs at both passage 3 and 5. Expression is presented as the average (+ s.d.) in arbitrary units with the P2 wild type set equal to 1 for each gene. Significance levels as determined by ANOVA are indicated above (* p<0.05, ** p<0.01, *** p<0.001).</p
