Figure 5

The breadth of expression correlated with the number of transcription factor binding sites. The breadth of expression correlated with the number of transcription factor binding sites in proximal promoters. This figure consists of five parts identified as a - e. Scatterplots were shown for ( a ) FANTOM5 human tissues, ( b ) FANTOM5 human primary cells, ( c ) FANTOM5 human cancer cell lines, ( d ) human data in Gene Expression Atlas [[51]]. The red line signified the linear model for the smoother line, while the blue line signified the non-linear model. Panel ( e ) provided an alternative illustration of the trend using a boxplot for the discretized breadth of expression in FANTOM5 tissues. Outlying tissue-specific genes with many transcription factor binding sites, which were likely enriched in inhibitory TFs, were marked in red. FANTOM5 tissues, primary cells and cancer cell lines were the three subsets of samples in FANTOM5 whose numbers were given in Table 1. Numbers of tags in FANTOM5 were normalized to tags per million (TPM). The TPM value of ten was chosen as a standard cutoff for a gene to be “on”. For Gene Expression Atlas, Affymetrix average difference (AD) higher that 200 classified a gene as “on” or expressed in a given tissue. Proximal promoters were defined by a symmetrical window of one kilobase in size around the transcription start site (+ − 500 bps from the TSS). As an additional control, we performed a randomization procedure where proximal promoters of all genes were shuffled. The value of the t-statistic for the strength of correlation in the observed dataset was compared against 10,000 datasets with randomized assignments between promoters and RefSeqs. The value of t-statistic for observed data (54.29404) was compared with t-statistics for 10,000 randomized datasets (mean −0.00959) and the P-value obtained was lesser than 2.2e-16.