Identify Inflammatory Bowel Disease-Related Genes Based on Machine Learning

Abstract

The patients of Inflammatory bowel disease (IBD) are increasing worldwide. IBD has the characteristics of recurring and difficult to cure, and it is also one of the high-risk factors for colorectal cancer (CRC). The occurrence of IBD is closely related to genetic factors, which prompted us to identify IBD-related genes. Based on the hypothesis that similar diseases are related to similar genes, we purposed a SVM-based method to identify IBD-related genes by disease similarities and gene interactions. One hundred thirty-five diseases which have similarities with IBD and their related genes were obtained. These genes are considered as the candidates of IBD-related genes. We extracted features of each gene and implemented SVM to identify the probability that it is related to IBD. Ten-cross validation was applied to verify the effectiveness of our method. The AUC is 0.93 and AUPR is 0.97, which are the best among four methods. We prioritized the candidate genes and did case studies on top five genes.

Clinical and Endoscopic Improvement of Inflammatory Bowel Disease with Curcumin Therapy: Experiences from Clinical Studies

“…8,9 Several predisposing factors which involving in IBD including genetic, gut dysbiosis, smoking, nutrition and diet, environmental pollution, and psychological stress. [8][9][10][11][12][13][14][15][16][17][18][19][20] Several genes have been discovered to be associated with IBD, such as NOD2, CARD9, CARD15, ATG16L1, IRGM, IL-23R, IL-12B, STAT3, MUC2, IL-10R, IL-10, XIAP, etc. Genes polymorphism which contributes to IBD are very significant of each other, but they are commonly related to inflammatory pathways of the disease.…”

“…Genes polymorphism which contributes to IBD are very significant of each other, but they are commonly related to inflammatory pathways of the disease. 9,13,14 Besides genes, IBD was also found to be correlated with ethnical factors, where certain ethnicities shows higher incidences of IBD while other ethnics shows the opposite. 15 Gut microbiota composition and its relation with IBD has been proven in many studies where dysbiosis is seem to be associated with intestinal inflammatory conditions.…”