Figure 6 of Brooks, Mol Vis 2011; 17:3034-3054.


Figure 6. Comparison of the current and previous data sets of differentially expressed transcripts of Nrl−/− versus wild type (WT) mouse retina. Overlap between the differentially expressed transcripts (DETs) identified in the current study and previous studies using mouse retinas from the same age and genotype was determined using the Mouse Genome Informatics (MGI) gene symbol as the identifier. The current study includes all mRNA transcripts identified with the Burrows-Wheeler Aligner (BWA) workflow (fold change ≥1.5 and p value <0.05). The 438 DETs of an Affymetrix microarray study [38] and 6,123 DETs from another RNA-seq study [54] with similar criteria were used for comparison with our study. Of the 438 DETs from the Corbo et al. [38] study, 157 transcripts are not significantly differentially expressed in our data, 11 are expressed below the fragments per kilobase of exon model per million mapped reads (FPKM) detection threshold of 1.0, and 38 do not map to the current annotations. Of the 6,123 DETs from the Mustafi et al. [54] study, 4,858 transcripts are not significantly differentially expressed in our study, 348 are expressed below our FPKM detection threshold of 1.0, and 62 do not map to the current annotations.