4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing hypersensitive site 2 of the murine beta-globin locus control region.
Unprocessed (not normalized) hybridization ratios were used for analysis. These ratios showed clusters of 20-50 positive 4C-signals along the chromosome template. To define the clusters, a running mean or running median was applied, using a window size of 29 probes (on average 60 kb). Obtained values were compared to the running mean/median performed across randomized data. This was done for each array separately. Consequently, all measurements were appreciated relative to the amplitude and noise of that specific array. The False Discovery Rate (FDR), defined as (no. false positives) / (no. of false positives + no. of true positives), was determined as follows: (number of positives in the randomised set) / (number of positives in the data). The threshold level was determined using a top down approach to establish the minimal value for which: FDR<0.05.
Data processing
The signal ratio 4C-sample/genomic DNA was calculated for each probe.
