Skip to main content
Figure 6 | BMC Bioinformatics

Figure 6

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

Figure 6

Evaluation of ChIPXpress ranking performance across different parameter combinations. Heat map of average normalized AUC scores for different combinations of ranking methods and ranking parameters across all datasets tested using CisGenome and TileProbe (left), Original and TileMap (middle), and MACS and MAT (right) to analyze the test ChIPx datasets. The ranking methods evaluated include GEO-only, ChIPx-only, and ChIPXpress using a combination of cutoff values of c = −∞ (All), -2, -1, 0, 1, 2, with ranking weights of w = 0, 0.1, 0.2, … , 1. Performance is measured by averaging the normalized AUC score (the area under the positive predictive value curve divided by the total plot area) across all tested datasets. Overall, the best performing ranking method and weight is ChIPXpress with c = 0 and w = 0.1.

Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us