An Integrative Genomic and Epigenomic Approach for the Study of Transcriptional Regulation (original) (raw)
Figure 5
Gene expression and H3K9 acetylation synergize to increase the number of differentially expressed genes identified.
Panel A: Dot plot of t scores from T-test for gene expression (x axis) and H3K9 acetylation (y axis). 1,359 genes were identified as differentially expressed and 374 as differentially H3K9 acetylated, with absolute t scores>4.5 (p<0.02). 44 genes crossed the threshold for both assays (upper right). 83 genes that passed H3K9 acetylation threshold displayed marginal t scores (>2 and <4.5) for expression, while 154 genes that passed expression threshold displayed marginal t scores (>2 and <4.5) for H3K9 acetylation. Differential expression of the former genes was validated as in Fig 4. Combining genes with marginal t scores (>2 and <4.5) for both platforms simultaneously yielded an additional 382 genes with positive correlation that would have been missed by both platforms (central square, red). For illustrating purposes, points corresponding to gene expression t scores>8 or H3K9 acetylation t scores>7 were excluded from the figure. Panel B: Bar graph illustrating synergism between the gene expression and H3K9 acetylation analyses. 1314 genes were identified only by gene expression, 329 by H3K9 acetylation alone, and 44 genes were captured by both platforms. After the integrated analysis, an additional 382 genes were identified. Panels C and D: Validation of fold enrichment for H3K9 acetylation by qChIP (panel C) and fold difference in expression by qRT-PCR (panel D) of 9 genes (6 test and 3 negative controls) identified by the integrated analysis that had been previously missed by both.