Figure 2 : In silico analysis of the 17q22 locus.

From: Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)

Figure 2

(A) Functional annotations using data from the ENCODE project. From top to bottom, epigenetic signals evaluated included DNase clusters, and ENCODE chromatin states (ChromHMM) and histone modifications in HMEC and MCF7 cell lines. The detailed colour scheme in chromatin states is described in the UCSC browser. All tracks were generated by the UCSC genome browser (hg 19). (B) Long-range chromatin interactions. From top to bottom, ChIA-PET data for Pol2 and CTCF in MCF7 cell lines. The ChIA-PET raw data available on GEO under the following accession (GSE63525.K56, GSE33664, GSE39495) were processed with the GenomicRanges package. -RNAseq data from MCF7 and HMEC cell lines. The value of the RNAseq analysis corresponds to the mean RPM value for COX11, TOM1L1 and STXBP4 from 4 HMEC and 19 MCF7 datasets, respectively. The annotation has been obtained through the Bioconductor annotation package TxDb.Hsapiens.UCSC.hg19.knownGene. The tracks have been generated using ggplot2 and ggbio library in R.