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Figure 5 | BMC Bioinformatics

Figure 5

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

Figure 5

Evaluation of ChIPXpress performance across different rankings weight for a set truncation cutoff of 0. Boxplot of the performance of different ranking methods for GEO-only, ChIPx-only, and ChIPXpress using weights of w = 0, 0.1, 0.2, … , 1. The TF expression cutoff is set to c = 0 for each weight tested. Performance is measured by the normalized AUC score (the area under the positive predictive value curve divided by the total plot area). This is equivalent to averaging the positive predictive values across the top 1 to n (100, 500, 1000) ranked predictions. Each individual point corresponds to a specific TF data set and the crosses correspond to the mean normalized AUC score across all datasets tested. CisGenome was used to analyze ChIP-seq data and TileProbe was used to analyze ChIP-chip data.

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BMC Bioinformatics

ISSN: 1471-2105

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