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Exploring Genome-wide Differences in DNA Methylation Profiles
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For instance, explore the methylation profile of the BARX1 gene, the sixth significant
gene with intergenic methylation in the previous list. The GTF formatted file
ensemblmart_barx1.gtf contains structural information for this gene obtained from
Ensembl using the BioMart service.
Use GTFAnnotation to load the structural information into MATLAB. There are two
annotated transcripts for this gene.
barx1 = GTFAnnotation('ensemblmart_barx1.gtf')
transcripts = getTranscriptNames(barx1)
barx1 =
GTFAnnotation with properties:
FieldNames: {1x11 cell}
NumEntries: 18
transcripts =
'ENST00000253968'
'ENST00000401724'
Plot the DNA methylation profile for both HCT116 sample replicates with base-pair
resolution. Overlay the CpG islands and plot the exons for each of the two transcripts
along the bottom of the plot.
range = barx1.getRange;
r1 = range(1)-1000; % set the region limits
r2 = range(2)+1000;
figure
hold on
% plot high-resolution coverage of bm_hct116_1
h1 = plot(r1:r2,getBaseCoverage(bm_hct116_1,r1,r2,'binWidth',1),'b');
% plot high-resolution coverage of bm_hct116_2
h2 = plot(r1:r2,getBaseCoverage(bm_hct116_2,r1,r2,'binWidth',1),'g');
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