The effect of neighbor genes on GFP expression. (A) Average GFP expression of all clones divided into two equally sized groups with either high (Hi-N) or low (Lo-N) neighbor gene activity. The 1.1-fold difference in GFP expression is not significant (P = 0.71). (B) Average GFP expression for both groups of Hi-N and Lo-N clones, each divided into two equally sized groups with either high (gray bars) or low (black bars) domain activity (window size 49). GFP expression differs 2.1-fold between both domain types for the Hi-N group (P = 0.02) and 2.3-fold between both domain types for the Lo-N group (P = 0.008). There is no significant difference in GFP expression between the Hi-N and Lo-N groups of the same domain type (P > 0.71). (C,E) Average domain activity per group of clones. Domain activity does not differ significantly between the Hi-N and Lo-N clones in C, or between the Hi-N and Lo-N clones of the same domain types in E. (D,F) Average neighbor gene activity per group of clones. The difference in neighbor gene activity is 9.9-fold between the Hi-N and Lo-N clones in D, but not significant between the different domain types of the Hi-N and Lo-N clones in F (P > 0.21). Neighbor gene activity was calculated as the average expression of the two immediate neighboring genes as measured by Affymetrix arrays. Domain activity was defined as the median expression of the surrounding 49 genes in 133 pooled SAGE libraries. Out of 90 clones, six have a pair of neighboring genes without a probe set and were therefore excluded from the analysis. Clone numbers in each group are thus: Hi-N (n = 42) and Lo-N (n = 42) for the analysis in A, C, and D and n = 21 for all four groups in B, E, and F. All P-values were calculated with an unpaired t-test. Error bars represent standard error of the mean.
