Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite
Fig 3
Gene set enrichment analysis (GSEA) of up-regulated genes between exon arrays and previously published 15K agilent array show high reproducibility of biological information.
GSEA plots for chip to chip comparisons of unregulated genes for HB3 12 hpi vs 36 hpi samples. Black lines indicate the location of “hits” from the rank order list of the up or down-regulated genes from the query list. Correlation values between ranked ordered and query list is progressively calculated and indicated by the red bar (with stronger correlations indicated by darker hue). The “zero crosses at” dotted line indicates when the enrichment score decays back to zero and there are no more potential matches between the query and rank ordered lists. (A and C) Comparing the top up-regulated and down-regulated genes on the Agilent 15K array to the rank ordered list of all genes on the Nimblegen exon array. (B and D) Comparing the top up-regulated and down-regulated genes on the Agilent HD exon array to the rank ordered differential expression of all genes on the comparably designed Nimblegen exon array. These comparisons show that the top up-regulated genes between 12 hpi and 36 hpi are consistent across all 3 platforms.