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Figure 7 | BMC Bioinformatics

Figure 7

From: ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking

Figure 7

PPV plot of ChIPXpress prediction performance when no matching gene expression data in PED is available. Plot of MYC expression compared to an example target gene, PPAT (A), and Gli3 expression compared to an example target gene, Nfatc4 (B), demonstrating similar levels of TF-TG correlation, even after removing all MCF7 and limbbud related cell types in the human and mouse PED compendium, respectively. Prediction performance of ChIPXpress (solid) rankings is compared to ChIPx-only (dot-dash) and GEO-only (dashed) rankings for MYC target genes in MCF7 cells (C), and Gli3 target genes in limbbud (D). The positive predictive value (PPV) is depicted for the top 50, 100, …, 1000 predictions In both analyses, all related cell types are removed from the compendium to simulate situations in which gene expression data related to the cell-type of interest is unavailable.

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BMC Bioinformatics

ISSN: 1471-2105

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