Hi Srinivas, The description pages also explains what the areas of color mean. In the case of this track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr22&g=wgEncodeRegMarkH3k4me1, it states that " A specific modification of a specific histone protein is called a histone mark. This track shows the levels of enrichment of the H3K4Me1 histone mark across the genome as determined by a ChIP-seq assay. The H3K4me1 histone mark is the mono-methylation of lysine 4 of the H3 histone protein, and it is associated with enhancers and with DNA regions downstream of transcription starts."
To summarize, the colors you are looking at are the areas of the genome that have various levels of the H3K4Me1 histone mark. I hope that clarifies what you are looking at. If you have further questions, please reply to: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: srinivas naidu kovvali <[email protected]> Date: Tue, Apr 17, 2012 at 10:19 AM Subject: Re: [Genome] one more querry To: Vanessa Kirkup Swing <[email protected]> Dr.vanessa i have seen this page this morning, and thanx for the same, what i am thinking is when i selected a particular cell line, the browser is showing its respective color, that means that regions is methylated in that cell line is the way i am going is correct?? sorry for sending too many simple queries, i am new to this site hope u can understand sincerely srinivas kovvali On 17 April 2012 22:40, Vanessa Kirkup Swing <[email protected]> wrote: > Hi Srinivas, > > Please see the description pages for each track that you are looking at > for information regarding the color conventions. Here is a link to the > track description page for hg19, Layered H3K4Me1 Track: > > > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr22&g=wgEncodeRegMarkH3k4me1 > > In this case, the color coding represents a particular cell line. > > If you have further questions, please email the list: [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: srinivas naidu kovvali <[email protected]> > Date: Tue, Apr 17, 2012 at 4:51 AM > Subject: [Genome] one more querry > To: [email protected] > > > Dear Dr. Steve Heitner, > > thank you very much for the immediate response which almost solved my > queries, however, a few thing are remaining > > here with again i am attahcing pdf of a browser, in that when i am looking > at H3K27AC, H3KME3, there is a scale, for examples 0 to 150 for H3K27AC, > 0 to 50 for h3kme3, where as i selected cell lines of my interest and > there are in blue orange colors, do these scales have any importance?? > appearing of the color as per the selected cell lines indicates that, that > particular region has methylation, this what i infer my self by seeing the > data. am i correct or do the scales have any significance?? > > kindly address these queries > > thanking you > > sincerely > > srinivas kovvali > > -- > Srinivas Kovvali J.R.F > Anthropological Survey of India, > Southern Regional center, > Mysore > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > -- Srinivas Kovvali J.R.F Anthropological Survey of India, Southern Regional center, Mysore _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
