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Figure 4 | BMC Genomics

Figure 4

From: Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast

Figure 4

Comparison of TF co-occupancy and absolute intensity among selected probe families and sub-families and different mapping criteria. TF co-enrichment M was defined for each probe as the median log2 fold enrichment across all rich media ChIP-chip experiments, and the family as the difference in mean M among probes in a family and all other probes. The p-value was calculated using a t-test. Similarly, the absolute intensity A for each probe in each experiment was defined as the mean (Lowess-normalized) intensity between the red and green channels; the median A was calculated across all experiments for each probe; and the family was reported as the difference in mean A among probes within a family and all other probes. Probe mapping and categories for comparison are as follows (see Methods for details of probe categorization): (A) Probes with high overlap vs. all other probes. (B) Probes with any overlap vs. all other probes. (C) Probes with low overlap or neighboring vs. non-neighboring probes (high overlap probes excluded from the analysis). (D) Neighboring probes vs. non-neighboring probes (probes with any overlap excluded from the analysis). Significant co-enrichment p-values are highlighted yellow; significant intensity p-values, which may signify cross-hybridization, are highlighted red.

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