Figure 4

Cumulative p-value distributions for each tag comparison made between SAGE libraries in the study. Monte Carlo analysis using binomial distribution was used to generate p-values for both observed and chance tag p-values. The software for carrying out this analysis is included in the SAGE 3.0.1 software package [18]. Differences are expressed as a cumulative fraction of the total tags for which comparisons could be made, which in this case is all tags present more than once in both libraries combined. Chance variation, the cumulative p-value difference expected for chance variation in sampling (values computed for comparison of SAGE libraries ONL1 vs ONL2 - the plot of chance cumulative p-value differences is essentially the same for each library comparison considered); sampling, ONL1 vs ONL2 (same library, different tags); ditag, P2.5A vs P2.5B (same ditag ligation, different libraries); mRNA, crx^+/+A vs crx^+/+B (same starting mRNA, different libraries); 44-year-old vs 41-year-old, libraries from peripheral retina from different similarly aged males; 88-year-old vs 44-year-old, libraries from peripheral retina from individuals who differ in age and sex; littermates, P6.5A vs P6.5B (libraries made from retinas of three P6.5 C57B/6 mice vs libraries made from retinas of three littermates); environment, hypothalamus A vs hypothalamus B (libraries made from hypothalami of 3 8-week-old male C57B/6 mice housed in Boston, MA vs libraries made from hypothalami of 20 8-week-old male C57B/6 mice housed in Melbourne, Australia); retina vs hypothalamus, libraries from adult male C57B/6 mouse retina vs adult male C57B/6 mouse hypothalamus; retina vs 3T3 cells, libraries from adult male C57B/6 mouse retina vs mouse 3T3 fibroblast cell line.