Django-based Web Interface for Differential Expression Analysis of RNA-Seq Data: A Case Study on Friedreich ataxia

Abstract

Next Generation Sequencing technologies such as RNA-Seq are now challeng- ing microarrays as the tool of choice for genome analysis. The bioinformatics analysis

of resultant data is time-consuming and challenging, especially for researchers having little knowledge of Linux command-line. In order to overcome this obstacle several desktop and web interfaces have been developed. These interfaces have shortcomings and technical difficulties. Very few of them cover all the steps of RNA-Seq analysis from data collection to differential expression which suggests the need to make in

house web interface for RNA-Seq data analysis. An interactive web interface, SE- QClick has been developed for RNA-Seq data analysis using python web framework

called Django. SEQClick is developed with an aim to ease the process of RNA-Seq data analysis which was previously time taking and required computational skills. SEQClick incorporates various utilities of 10 bioinformatics tools which perform the

required steps of RNA-Seq data analysis. Currently, SEQClick can only perform dif- ferential expression using DESeq2 and Ballgown on test data. RNA sequencing and

small RNA sequencing datasets of Friedreich ataxia were used as a case study. Friedre- ich ataxia is a rare neurodegenerative disease that predominantly affects the nervous

systems and the heart. Its is an autosomal recessive disorder caused by mutation in FXN gene. RNA-Seq analysis was performed on these datasets and differentially expressed genes were identified. After which pathway analysis was performed using

common differentially expressed genes in order to find out the key factors and phe- nomenon of disease progression. In future we aim to give user the freedom to use his

own data in DESeq2 and Ballgown and select his own normalization, standardization

and plotting options. We also aim to increase the diversity of SEQClick by incorpo- rating more bioinformatics tools and giving more parameter selection options to the

user. Also the reference genomes of other organism can be incorporated to increase the scope of SEQClick to animal studies.