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. Author manuscript; available in PMC: 2013 Dec 20.
Published in final edited form as: Nat Biotechnol. 2012 Dec 9;31(1):10.1038/nbt.2450. doi: 10.1038/nbt.2450

Figure 5.

Figure 5

Changes in expression of cell cycle regulatory genes in response to HOXA1 knockdown. (a) GSEA analysis of the knockdown for selected REACTOME gene sets. (b) Cuffdiff 2 reports an increase in CDK2 expression, which is attributable to a single isoform that includes the full activation loop, a feature required for maximal CDK2 activity. KD, knockdown. (c) Cuffdiff 2 reports a decrease in ORC6 expression, which is attributable to a single isoform that includes the full suite of residues required for optimal DNA binding not present in the minor isoforms arising from the gene. (d) Cuffdiff 2 reports an increase in TBX3 attributable to a single isoform lacking an exon situated within the T-box DNA binding domain that is present in a highly similar minor isoform. (e) Cuffdiff 2 reports a decrease in CDC14B attributable to decreases in the two major isoforms. Error bars indicate 95% confidence intervals in expression. (f) Changes in isoform expression reported by Cuffdiff 2 compared against measurements made with isoform-specific qPCR. The black line indicates perfect correspondence between the two platforms. The orange line is a linear regression through all points, and the red line excludes the three major outliers, which target low abundance isoforms, two of which cannot be distinguished from primary transcript or genomic DNA. DE, differentially expressed.