Figure 2.

COGRIM improves gene classification in HAP4 case. For each of HAP4 gene clusters, genes are ordered by the ChIP binding P value obtained from Lee and coworkers [3]. (a) The expression profile of HAP4, a well characterized factor that is involved in respiration, across approximately 500 experiments. (b) The B+/C- gene cluster (33 genes). With ChIP binding data alone, these genes are considered HAP4 targets but they do not share similar expression patterns (averaged centered pearson correlation is only 0.06) and none of them was assigned to the MIPS respiration category. COGRIM does not consider these genes as HAP4 functional targets. (c) The B+/C+ gene cluster (34 genes). This gene cluster shows high expression correlation (the averaged centered pearson correlation is 0.56), and 23 out of 34 genes were assigned to the MIPS respiration category. (d) The B-/C+ gene set (17 genes). These 17 genes were not identified as HAP4 targets by using binding data alone (with P value threshold 0.001) but were predicted by COGRIM to be functional targets. They exhibit coherent expression (the averaged centered pearson correlation is 0.60) and nine of them (ybl030c, ydl004w, yfr033c, yjl166w, yjr048w, ykl141w, ykl148c, yml120c, and ynl055c) are involved in respiration. ChIP, chromatin immunoprecipitation.