RESEARCH ARTICLE A Powerful Statistical Approach for Large- Scale Differential Transcription Analysis

Next generation sequencing (NGS) is increasingly being used for transcriptome-wide analy-sis of differential gene expression. The NGS data are multidimensional count data. There-fore, most of the statistical methods developed well for microarray data analysis are not applicable to transcriptomic data. For this reason, a variety of new statistical methods based on count data of transcript reads have been correspondingly proposed. But due to high cost and limitation of biological resources, current NGS data are still generated from a few replicate libraries. Some of these existing methods do not always have desirable perfor-mances on count data. We here developed a very powerful and robust statistical method based on beta and binomial distributions. Our method (mBeta t-test) is specifically applica-ble to sequence count data from small samples. Both simulated and real transcriptomic data showed mBeta t-test significantly outperformed the existing top statistical methods chosen in all 12 given scenarios and performed with high efficiency and high stability. The differentially expressed genes found by our method from real transcriptomic data were vali-dated by qPCR experiments. Our method shows high power in finding truly differential ex-pression, conservatively estimating FDR and high stability in RNA sequence count data derived from small samples. Our method can also be extended to genome-wide detection of differential splicing events