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Fig. 2 | BMC Medical Genetics

Fig. 2

From: Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

Fig. 2

Epigenetic prediction of gene expression to identify PQS positions correlated with altered gene expression. a Correlation of log2-transformed epigenomic track signals with log2-transformed gene expression represented as a function of location 1 kbp upstream and downstream of TSS. Bin size is 100 bp. Prior to log2-transformation, 0.25 % of the maximal bin value was added to each bin feature to avoid the log2(0) issue. b Representative correlation of CAGE TSS-specific gene expression measurements with epigenetic model predictions generated through Bayesian linear regression. Models were trained on datasets containing half of all PQS-free TSS in the human genome. Gene expression predictions were then generated for the remainder of the PQS-free TSS. c Analysis of model prediction error as a function of PQS position, assigned to sense (S) and antisense (AS) strand effects. Prediction error estimates were sorted into 200-bp bins iterated at a 10-bp interval, based on the position of the PQS nearest to the TSS, and then compared to the prediction error estimates for PQS-free TSS using 1-way ANOVA. The top panels show the p-value from this analysis as a function of position with respect to the TSS. The dashed line represents the p-value threshold used for determining statistical significance in the analysis. The bottom panels show prediction error averages for the binned values. Areas with shaded peaks represent locations where the p-value is statistically significant for rejection of the null hypothesis. Prediction error value > 0 represent positions where PQS presence correlates with higher gene expression. Prediction error values < 0 represent positions where PQS presence correlates with lower gene expression. d Aggregate map of all statistically-significant positions from prediction error analysis based on seven human cell lines

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