Table 1.
Human subjects.
Figure 1.
CpG islands are differentially methylated in IPF and control samples
(A) Human CpG Island Microarray data: the heatmap on the left is the visual comparison of global methylation profiles between the 10 Control and the 12 IPF samples. The heatmap on the right consists only of the differentially methylated CpG probes highlighted by the red rectangle (p-value < 0.05, FDR<5%). Methylated CpG islands are shown in progressively brighter shades of yellow, depending on the fold difference, and hypomethylated CpG islands are shown in progressively brighter shades of purple. Grey stands for no difference between the two sample groups being compared. (B) EpiTYPER confirmation of differentially methylated CpG islands. Bars represent the average methylation of all the samples per study group. The X-axis shows the genomic location of each CpG island and Y-axis shows the percentage of methylation.
Table 2.
Functional annotation clustering of differentially methylated CpG islands.
Table 3.
Differentially methylated promoters between IPF and control samples.
Figure 2.
Expression of genes with differentially methylated promoters.
qRT-PCR assay on 3 genes with hypomethylated promoter-associated CpG islands showed increase in the expression of the downstream gene. Y-axis shows fold change of detected transcripts in IPF samples when the expression in controls is set to baseline equal to 1. * denotes p-values <0.05. Error bars are based on Standard Deviation.
Figure 3.
Comparison of IPF and Adenocarcinoma to control samples.
(A) 3-D plot representation of the results after Principal Component Analysis of all 3 sample groups. Each color-coded dot represents a sample (red-control, green-IPF and blue-cancer) and each sample is positioned in the 3-D space according to its similarity or difference to the others. (B) Comparison of differentially methylated CpG islands that overlap between IPF and Lung Cancer. The heatmap consists of 402 differentially methylated CpG islands that are found to overlap between IPF and Lung Cancer. High methylation levels of a CpG islands are shown in yellow while low methylation levels of methylation are shown in purple. Grey stands for no difference between the two groups being compared.
Figure 4.
Methylation profile of LINE-1 retrotransposon.
Global methylation levels of the LINE-1 retrotransposons were defined using the EpiTYPER mass array assay. Each bar represents the methylation in one of the 15 CpG dinucleotides or CpG units that span the LINE-1 sequence. Methylation levels are calculated as the average of all samples in each group (Control, IPF, Cancer) and standard error bars are included. The X axis shows the CpG dinucleotide or the CpG unit and the Y axis shows the percentage of methylation. The LINE-1 promoter is indicated in purple. The red arrowheads indicate units of 2-3 CpG dinucleotides.