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. Author manuscript; available in PMC: 2010 Feb 19.
Published in final edited form as: Nat Genet. 2007 Nov 11;39(12):1512–1516. doi: 10.1038/ng.2007.26

Fig. 2. Whole-genome analysis of Pol II binding.

Fig. 2

(A) Genes were assigned to either one of three classes - stalled Pol II, active Pol II or no Pol II, and - based on their Stalling Index (box). The Stalling Index is the ratio between the maximum enrichment near the transcription start site (maxTSS) (± 300 bp) and the median enrichment of the probes distributed across the transcription unit (mediantranscript) (excluding the first 600 bp). Stalling Index values of >4 qualified as “stalled Pol II”, whereas Stalling Index values <2 qualified as “uniform (active) Pol II”. If no probe within the TSS region was significantly bound, the gene was assigned to the “no Pol II” category. (B) Over 76% of all protein-coding genes could be assigned to one of three categories based on Stalling Index values: 12% have stalled Pol II, 23% display the active form of Pol II and 37% of genes have no Pol II. Among the genes with stalled Pol II, 62% have Pol II tightly restricted to the transcription start site.