Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data
Figure 4
Consistency of target gene predictions.
Independent ChIP-seq experiments are available for some of the factors measured in the hematopoietic system. Consistency of target predictions is quantified as the overlap between the top 500 target genes. Results are summarized based on intersecting targets from pairs of ChIP-seq experiments measuring the same transcription factor (‘same TF’), using ChIP-seq experiments from different factors, but the same system (hematopoietic cells, ‘HemoChIP’) and using ChIP-seq experiments from a different system (ES cells, ‘ESChIP’). Numbers on the right are rounded p-values, measuring the significance of the difference between the overlaps (t-test). P-values for the comparison ‘same TF’ versus ‘HemoChIP’ are generally less significant than ‘HemoChIP’ versus ‘ESChIP’, because the number of comparisons (observations) is smaller.