Figure 3

Visualization of TXNL2. Top: UCSC Genome Browser view of TXNL2 probe alignments alongside AceView transcripts. The probes and transcripts they target are outlined by color; Agilent is green, Affymetrix is blue. Bottom Left: Heatmap visualization of the gene according to pairwise Euclidean distance. The Agilent probes, outlined in green, form a dark block, indicating their measurements are close together. The Affymetrix probes do not show any grouping pattern. Bottom Right: Log2 signal intensity of the replicates. The Affymetrix probes, outlined in blue, show low signal intensity and a random distribution of control and experimental signals from probe to probe, which explains the lack of visual pattern in the heatmap. The Agilent probes, outlined in green, show clear separation between the control and experimental groups, indicating a downregulation of TXNL2. Real-time PCR showed the Affymetrix transcript to be absent in the sample, while the Agilent transcripts were validated to be downregulated, explaining the signal patterns.