Figure 6.

Comparisons between jMOSAiCS and chromHMM based on data simulated from ChIP-seq experiment of STAT1 in HeLa3 cells (setting SE2). (a) Identification of combinatorial patterns: 11: enriched in both samples; 10: enriched only in sample 1. True: number of enriched regions; chromHMM: results by original four-state chromHMM; chromHMM-true: four-state chromHMM coupled with true binary data for the bins; chromHMM-0.05: four-state chromHMM coupled with MOSAiCS binarization of the bins at an FDR of 0.05; chromHMM-0.2: four-state chromHMM coupled with MOSAiCS binarization of the bins at an FDR of 0.2. (b) Accuracy of enrichment detection at the region (B) and dataset-specific region (E1 and E2) levels by jMOSAiCS and two-state chromHMM. ChIP: chromatin immunoprecipitation; FDR: false discovery rate; FP: false positives; jMOSAiCS: joint model-based one- and two-sample analysis and inference for ChIP-seq TP: true positives

Zeng et al. Genome Biology 2013 14:R38   doi:10.1186/gb-2013-14-4-r38
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