ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements
Fig 2
ChIP-GSM and competing methods abilities to infer TF modules using realistically simulated ChIP-seq data.
We simulate ChIP-seq read counts for 100,000 regions and examine the accuracy of module inference by applying each competing method to a low challenging case (Case 1, four TFs), a middle challenging case (Case 2, seven TFs) and a high challenging case (Case 3, eighteen TFs). (A) F-measure of each method on module inference across all regions; (B) F-measure of each method on regions with at least one weak binding event. ChIP-GSM performs better than the comparable methods, especially when there are many TFs with weak binding events.