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==Discussion== [[File:5fC_Figure1.pdf]] A) Genome browser snap shot of wig files around a called peak. B) Pie charts showing base pairs genomic distribution of all significant peaks (FDR<5%) with annotated genomic regions. C) Using wig files from input and IP, the mean occupancy of reads a 100bp sliding window around each of ~19K promoters were calculated. The mean values from input were subtracted from mean values of IP. Genes were separated into 5 groups based on the expression level of replicate #1 in the [GSE13805 | http://www.wip.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE13805] study on mouse ESCs. * More peaks were found in knockdown than in wildtype, this supports that the knocked-down protein is responsible for converting 5fC into something else. * In both control and knockdown, enrichment of peaks were in introns or other genomic regions and depletion of peaks (p<0.05) were in exons. * In wildtype, occupancy of 5fC around promoters were not correlated with gene activity. * In knockdown, occupancy of 5fC around promoters appears to be correlated with gene activity. Higher densities of 5fC were found towards the 5'UTR region of the gene than upstream of TSS.
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