Schematic diagram of our data binning and supervised analysis. (a) DNA regions around the transcription start site (TSS) and transcription terminal site (TTS) of each transcript were separated into 160 bins of 100 bp in size. Average signal of each chromatin feature was calculated for all transcripts, resulting in a predictor matrix for each bin. These predictor matrices were used to predict expression of transcripts by support vector machine (SVM) or support vector regression (SVR) models. The genome-wide data for chromatin features and gene expression were generated by the modENCODE project using ChIP-chip/ChIP-seq and RNA-seq experiments, respectively. (b) A summary of datasets used in our analysis. L, larval; TF, transcription factor; YA, young adult.
Cheng et al. Genome Biology 2011 12:R15 doi:10.1186/gb-2011-12-2-r15