Transcriptomic database for IBD

Active:

true

Description

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder characterized by damage to the intestinal mucosa (https://www.mdpi.com/2227-9059/10/7/1695). In terms of etiology, IBD comprises a group of chronic inflammatory diseases [e.g., ulcerative colitis (UC) and Crohn’s disease (CD)] characterized by damage to the intestinal mucosa, which is believed to be caused by a combination of factors, including abnormal immunity of the intestinal mucosa. In accordance with the abnormal autoimmune function in patients with IBD, the gut and other organs and tissues may be damaged and may be susceptible to cancer development. Although recent studies have described substantial advances in our understanding of the molecular pathogenesis of IBD, the mechanism remains unclear. To elucidate the disease mechanisms, RNA sequencing (RNA-seq) technology has been used to survey global transcriptomic changes in IBD. Although RNA-seq captures expressions of transcripts other than protein-coding genes, the expressions of non-protein-coding RNAs [e.g., long non-coding RNAs (lncRNAs)] have not been examined carefully. To fill this gap in knowledge, we will re-analyze the published RNA-seq data of IBD patients compared to the healthy donors to catalog lncRNA expressions. As there is no expression database focused exclusively on IBD, we will make a knowledge database for both protein-coding and lncRNA genes in IBD in this project. The database architecture will be similar to our previous databases, FibroDB (https://rnamedicine.shinyapps.io/FibroDB/) and LiverDB (https://rnamedicine.shinyapps.io/LiverDB/).

R

RNA-Seq, Data mining, R-Shiny

Project Stage

Late

Avg. Hours / Week

6

Project Provider

Shizuka Uchida, PhD

Commitment (Months)

3

Spots Open

1

Project Lead

TBD

Publication if successful?

Yes

Trainee authorship criteria (if applicable)

The BRN trainees will be co-authors.

Required Skill Assessments

Basic Data Science Web Development

R Programming

Linux for Bioinformatics

RNA-Seq Analysis

R for Data Science