Figure 7. An example of a false differentially expressed gene. A: Expression level of Anapc1 mRNA (y-axis) across the BXD strains (x-axis) from the Department of Defense (DoD) database (Probe_17391461). B: Probe verification at UCSC demonstrates that there is a single nucleotide polymorphism (SNP; rs27412956) in the probe coverage area which may lead to mis-binding toward the D2 sequence. C: This gene is identified as not differentially expressed in the RNA sequencing (RNA-seq) data. Viewing the RNA-seq signal in the Integrative Genomics Viewer (IGV) browser shows equal expression between the two stains across all exons, indicating that this is a false positive differentially expressed gene using microarray methodology.