PPV plot comparing prediction performance of ChIPXpress to ChIPx-only rankings and GEO-only rankings. Prediction performance of ChIPXpress (solid) rankings compared to ChIPx-only (dot-dash) and GEO-only (dashed) rankings for MYC target genes in MCF7 cells, Oct4 target genes in embryonic stem cells (ESCs), Jarid2 target genes in ESCs, and Gli3 target genes in limbbud. The positive predictive value (PPV) is depicted for the top 50, 100, …, 1000 predictions. Three different peak technologies are evaluated for each TF: (left-right) ChIP-seq, (column 1-2), ChIP-chip whole genome tiling arrays (column 3), and ChIP-chip promoter arrays (column 4). Three different sets of peak callers are also tested for each TF: (A) CisGenome for ChIP-seq, and TileProbe for ChIP-chip, (B) Original (the peaks reported by the original publication) for ChIP-seq, and TileMap for ChIP-chip, and (C) MACS for ChIP-seq, and MAT for ChIP-chip.