Differing types of DEGs found by RNA-Seq and microarray data (Panels A–D).

<p>Numbers of reads in RPM (reads per million mapped reads) are shown on the Y-axis and the genomic region is displayed on the X-axis using a common NCBI scale for representative AFB1 (blue reads) and CTRL (black reads) sample tracks in UCSC browser format. Placements of microarray probes for specific transcripts are indicated by small rose-colored squares with probe names below. Numbered Cufflinks assembled transcripts and the corresponding RefSeq (gene abbreviation) or Ensembl annotated transcripts (ENSRNOT) identifiers are displayed under the RNA-Seq tracks. Exons are represented as blocks or bands; introns are lines between exons. Arrows at the end of assembled or annotated transcripts show the direction of transcription. Open arrows in specific panels point out a new Cufflinks identified exon. Bar graphs to the right show mean fold changes (AFB1/CTRL) for specific microarray probes and the corresponding RNA-Seq transcripts (DESeq). At the bottom of Panels A and C, the entire transcript (red) is presented for which a portion of the transcript which has been enlarged (blue bracket) for the RNASeq tracks shown above. In Panel D, only spliced EST’s (parallel lines in the center of spliced EST represent gaps in the alignment) were available which were without RefSeq or Ensembl transcript annotation and for which no microarray probe had been assigned. In Panel D bar graph, fold changes for two separate Cufflinks transcripts are indicated while no microarray data were available (no probe).