JIL-1 and Transcriptionn Figure 1. JIL-1 is a mark for gene activity and for dosage compensation in SL2 cells. High resolution ChIP on chip profiles of JIL-1, ePol, H4K16ac and H3K36me3 [30]. The data is represented as average log2 signal ratio of IP over input. Bars are coloured when the signal is above zero. The dark grey line toping each profile represents the mean signal within a 500 bp window centred on the probe. High affinity sites (HAS) for the DCC according to [29] are depicted as red boxes above the gene annotations. A representative 250 kb portion has been selected (A) for the X chromosome and (B) for chromosome 3R. (C) Fractional distribution of oligonucleotides according to genomic features is shown for all probes on the array (n = 384680) and compared to the ones within JIL-1 (n = 112954) and ePol (n = 125303) binding regions as determined by hidden markov modelling. (D) The density per gene was defined as the average ratio (IP/input) of probes within a gene. The densities of ePol on autosomal genes (labelled A) and X-linked genes (labelled X) in a box plot representation. Activity status was determined by microarray expression profiling. (E) JIL-1 densities on the same sets of genes as in D, the median values for active autosomal and X-linked genes are given. The boxplot representation in all figures define 25th to 75th percentiles (boxes), 50th percentile (lines in boxes), and ranges (whiskers, 1.5 times the interquartile range extended from both ends of the box). Outliers were removed from the analysis. doi:10.1371/journal.pgen.1001327.g001 PLoS Genetics | www.plosgenetics.org 3 March 2011 | Volume 7 | Issue 3 | e1001327