Hello, Srinivas. I believe you are looking at the hg19 Broad Histone track. In most ENCODE tracks, the color scheme is based on the cell line in question. Tier 1 and tier 2 cell lines (GM12878, H1-hESC, K562, HeLa-S3, HepG2 and HUVEC) are always represented by some non-black color while other cell lines are almost always colored black. In these tracks, the colors are only meant to distinguish the tier 1 and tier 2 cell lines from other cell lines. They don't have any specific meaning.
Some other ENCODE tracks, such as GENCODE, have different color schemes. The description pages of the various tracks often contain an explanation for such things. It's always good practice to briefly read through the track description pages to see if they answer your questions. When you say that some tracks are thick compared to other tracks, it all depends on how you have configured your views. In the Broad Histone track, each experiment has a Peak subtrack and a Signal subtrack. By default, Peaks are set to display in pack mode and Signal is set to display in full mode, but you can change these settings at the top of this page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone. The Peak subtrack is displayed as a bar while the Signal subtrack is what is called a "wiggle" track. When viewed in full or pack display mode, a wiggle track appears at varying degrees of thickness and resembles hills or mountains. In squish or dense mode, a wiggle track is also displayed as a bar. Please see the Display Conventions and Configuration section and the Methods section at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone for a description of the Peaks and Signal subtracks. You also mentioned an instance where a track was displayed in pink and then became black. These tracks are actually meant to be displayed in all black, but the pink region indicates that there is data that is not being displayed because of the current display settings. For instance, if you look at the Osteoblast H3K27me3 Signal subtrack at chr21:33,034,242-33,034,818, you will see a small pink line at the left and right sides of the block of data. If you look at the left side of the Browser, you will see that the vertical viewing range for this subtrack is 1-50 (the default range for Signal subtracks). At the points where you see pink instead of black, the data values are actually smaller than 1 (the same would occur if there were values over 50 - see chr21:34,443,765-34,445,357). If you click on the block of data itself, you will see that the minimum value here is 0.16. If you change the Signal vertical viewing range to 0-50 by right-clicking the data block and selecting "Configure Osteobl H3K27me3", the range that was displayed in pink will now be displayed in black. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of srinivas naidu kovvali Sent: Monday, April 16, 2012 5:27 AM To: [email protected] Subject: [Genome] query using encode tracts for methylations Dear Sir, As part of my work i am UCSC genome brower to analyse the p4ha3 gene, where encode tracts are totally confusing for me. i am a very amateur in using UCSC genome browser, i found it difficult to understand the methylation patterns of encode tracts, particularly i am interested in methylation data from Osteobi ctcf, Osteobl H3K4me1, Osteobl H3K27me3 and few similar tracks, few track are displayed in pink and few are in balck, what does this color differentiations imply? also Osteobi H3K27me3 track is thick when compared to other tracts, few tracks have pink color upto certain length and there after they are black. can your kindself address these problems? it would be of great help to my research if you could answer these queries thanking you sincerely srinivas kovvali Srinivas Kovvali J.R.F Anthropological Survey of India, Southern Regional center, Mysore INDIA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
