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Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
Published on: June 21, 2016
Predicting gene expression level by the transcription factor binding signals in human embryonic stem cells
Lu-Qiang Zhang1, Qian-Zhong Li1, Wen-Xia Su1
1Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
Abstract:
The transcription factor (TF) binding signals play important role in the control of gene expression. In this study, to elucidate the relationship between the transcription factor binding signals and gene expression, we firstly analyze the distributions of 57 kinds of TFs' binding signals in human H1 embryonic stem cells. Their distributions in highly and lowly expressed genes are further compared. On this basis, a statistic model of predicting gene expression level is constructed by using 57 kinds of transcription factor synthetic indexes (TFSIs). Then, the TF's Down-regulated and Up-regulated genes are predicted and the statistics significance is estimated by one-sided Kolmogorov-Smirnov test. Based on the stepwise regression analysis, the "optimal" TFSIs are selected out, and the better results for predicting the expression level of genes with high CpG content promoters (HCPs) and low CpG content promoters (LCPs) are obtained.
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