deep Learning of the tissue-regulated splicing code

Introduction

Alternative splicing(AS) is a regulated process during gene expression that enables the same gene to give rise to splicing isoforms containing different combinations of exons, which leads to different protein products. Furthermore, AS is often tissue dependent. This paper mainly focus on performing Deep Neural Network (DNN) in predicting outcome of splicing, and compare the performance to formerly trained model Bayesian Neural Network (BNN) and Multinomial Logistic Regression (MLR). A huge difference that the author imposed in DNN is that each tissue type are treated as an input; while in previous BNN, each tissue type was considered as a different output of the neural network. Moreover, in previous work, the splicing code infers the direction of change of the percentage of transcripts with an exon spliced in (PSI). Now, this paper perform absolute PSI prediction for each tissue individually without averaging across tissues, and also predict the difference PSI ([math]\displaystyle{ delta }[/math]PSI) between pairs of tissues. Apart from regular deep neural network, this model will train these two prediction tasks simultaneously.