1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
A new reconstruction of mouse metebolic model using orthology-based approach
Paper ID : 1482-ICB10
Authors:
Saeideh Khodaei1, Yazdan Asgari2, Mehdi Totonchi3, Mohammad Karimi-Jafari *1
1Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
2Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
3Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
Abstract:
A genome-scale metabolic (GSM) model is an in silco metabolic model including chemical reactions that take place inside a cell, tissue, or organism. In a GSM model, gene- protein reaction rules represent the mapping between gene encoding enzymes and the reaction they catalyze. These rules are a fundamental component in orthology-based model to reconstruct a new GSM model of a target organism through a GSM model of a reference organism.
In this study, we reconstructed a new mouse GSM model (iMM1865) from human Recon3D model. For this purpose, we used homologous gene mapping and extracting mouse specific reactions through literature and databases. iMM1865 has been validated using 431 metabolic objective functions which were created to verify Recon3 model. This model with no dead-end metabolites and blocked reactions is more comprehensive than previous reported mouse models. Also it has passed more metabolic objective functions tests. Furthermore, to evaluate of the predictive ability of the model, gene essentiality simulations was performed.
Keywords:
genome-scale metabolic model, orthology-based reconstruction, Mouse metabolic model, iMM1865, Recon3D
Status : Paper Accepted (Oral Presentation)