Figure 1.
Lichen planus mRNA/miRNA expression patterns.
Cluster analysis of mRNAs (A) and miRNAs (B). Expressed features are represented in rows while patients are represented in columns. The heat map is color-coded according to the relative expression. Vertical dendograms display the similarity between the expressed features and horizontal dendograms display the similarities between the patients. Features are labeled with gene symbols (or with public references, if no gene symbols are available or with the genomic alignment where no public references are available) or with miRNA names, respectively. Multiple appearances of expressed features (e.g. OR2J2) are a result of one gene being represented by multiple transcripts which were all differentially expressed. Samples are labeled with H1–H7 for healthy individuals and L1–L7 for Lichen Planus patients.
Figure 2.
Principal component analysis of lichen planus patterns.
The two strongest components (X-axis: PCA1, Y-axis: PCA2) are shown for a PCA based on differentially expressed transcripts (A) and based on differentially expressed miRNAs (B). Each data point on the plot represents one healthy individual (light gray, labeled H1–H7) or one Lichen Planus patient (dark gray, labeled L1–L7).
Figure 3.
Enriched and depleted biological processes in lichen planus.
Biological processes (retrieved from the Gene Ontology Consortium) associated with differentially expressed transcripts (A) or grouped into most prominent categories (B). Level 1 terms (e.g. “system process” or “signal transduction”) were omitted. Each regulated item was associated to its biological processes using Gene Ontology, the resulting hits were summarized for each category of biological processes, illustrated by individual elements in the pie-chart. Similarly, biological processes (C) and categories (D) are shown for differentially expressed miRNAs. Numbers next to biological processes and categories indicate the number of transcripts or miRNAs observed.
Figure 4.
Genomic map of regulated transcripts and miRNAs in lichen planus.
A non-linear display of the genomic location is plotted on the X-axis, while the length of each chromosome plotted is determined by the amount of features identified in the chromosome. The significance is plotted as –log(P) on the y-axis for regulated transcripts and miRNAs in the corresponding genomic location. Data points are color-coded by fold change.
Figure 5.
Selected candidate transcripts under potential miRNA control.
5A) Regulated miRNAs (first row) are displayed with their predicted target mRNA (second row), in which the miRNAs were up-regulated when comparing lichen planus patients with healthy individuals, and their predicted target transcripts were down-regulated (left panel: initial screening; right panel: validation via real-time PCR). The y-axis displays the relative expression normalized to beta-actin (for mRNAs) or to small nucleolar RNA, C/D box 47 (SNORD47, for miRNAs). Error bars represent the standard error of the mean. 5B) The observed correlation between screening and validation results (rho = 0.765) is compared to expected correlations (based on a k = 10.000 Westfall and Young permutation). 1) Transcripts, where real-time PCR validation does not support initial screening results 2) KCNJ1 did not result in detectable signals in the validation step.