Zebasil Teshale (Mentor: Dr. Peter McGarvey, Protein Information Resource, Georgetown University)
August 26th, 2:40pm-3:00pm Room 1300, Harris Building.
Gene-disease networks provide essential information in the study of relationship between diseases. This project focuses on Immune related adverse events mentioned in “Application of the immunological disease continuum to study autoimmune and other inflammatory events after vaccination” Koenig et. al 2011 paper. The Genetic Association Database (GAD) and Online Mendelian Inheritance in Man (OMIM) were used to collect the required datasets. The main goal of this project is to generate a gene to immune related adverse event network and analyze genes and pathways involved using Cytoscape plugins for further study.
For the purpose of this project datasets were downloaded from GAD, OMIM and mapped to Unified Medical Language System (UMLS) terms. These files downloaded from OMIM and GAD was parsed using a code written in python to extract gene symbol, disease term, CUI number and pubmed IDs. Additional code is written which picks selected immune related adverse events and genes associated to them from the previously parsed files. The disease names were then mapped to UMLS terms. This data was supplemented with additional data previously extracted from Immune Epitope Database (IEDB) and UniProt. With the help of Cytoscape, a gene-disease network is generated and analyzed using ReactomeFI and other Cytoscape plugins.
The analysis showed some similarities with the classification of immune related events mentioned Koenig et. al 2011. The classifications suggested in the article partially coincide with the analysis performed using the ReactomeFI plugin. The relationship between the diseases was seen in the genes they share as well as the pathways they are involved in. Immune related adverse events in the group classified as Intermediate (MHC CLASS I) in the Koenig et. al 2011 paper, showed 17 genes and 51 pathways in common. The least number of common genes and common pathways seen in the group classified as Immediate Hypersensitivity ( IgE mediated) with 2 and 3 respectively.
Although further study is needed, the analysis resulted in adequate information on the immune related adverse events. The produced data can be used in specific research on immune related adverse events.