Example of histone modification profiles across ENCODE regions. (A) Screenshot from the UCSC genome browser (Hinrichs et al. 2006) of ENCODE region ENr333 (human chromosome 20: 33,304,929–33,804,928 bp, NCBI 35) showing ChIP-chip data for the lymphoblastoid cell line, GM06990, using five antibodies for the histone modifications H3K4me1, H3K4me2, H3K4me3, H3ac, and H4ac. The scale in base pairs is indicated by the vertical ticks at the top. The top track shows the UCSC known genes (Hsu et al. 2006) with transcriptional orientation and exons indicated by arrows and vertical ticks, respectively. Below is a track indicating the extent of the ENCODE region ENr333. ChIP-chip data are displayed in the five subsequent tracks as the median value of the ratio of normalized ChIP-chip sample fluorescence to input DNA fluorescence. Each black vertical bar is the enrichment measured at a single amplicon on the ENCODE PCR product microarray with the enrichment represented by the height of the bar. Five tracks represent the data for the five antibodies used in ChIP-chip as indicated by the label at the left of each track. Note that each track is dynamically scaled according to the data displayed, and hence comparison between tracks must take into account the enrichment scale at the left of each data track. (B) Screenshot as in A of ENCODE region ENr333 for ChIP-chip data using the antibody for H3K4me3 with the five cell lines as indicated at the left of the data tracks. The screenshot is aligned to the scale in panel A. Note that the GM06990 data are the same as are displayed in the third data track in panel A. (C) Screenshot of ChIP-chip data for ENCODE region ENm010 (the HOXA cluster on human chromosome 7: 26,730,761–27,230,760bp, NCBI35). At the top is the GENCODE reference gene annotation (Harrow et al. 2006). Data tracks are shown as in panels A and B for all ChIP-chip data on cell lines GM06990, K562, HeLa-S3, and HFL-1. Note the browser is zoomed in to show the HOXA cluster and does not show the full extent of ENm010.
