Investigating regulatory signatures of human autophagy related gene 5 (ATG5) through functional in silico analysis
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Date
2016
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Journal ISSN
Volume Title
Publisher
Elsevier B.V.
Abstract
Autophagy is an essential, homeostatic process which removes damaged cellular proteins and organelles for cellular renewal. ATG5, a part of E3 ubiquitin ligase-like complex (Atg12-Atg5/Atg16L1), is a key regulator involved in autophagosome formation - a crucial phase of autophagy. In this study, we used different in silico methods for comprehensive analysis of ATG5 to investigate its less explored regulatory activity. We have predicted various physico-chemical parameters and two possible transmembrane models that helped in exposing its functional regions. Twenty four PTM sites and 44 TFBS were identified which could be targeted to modulate the autophagy pathway. Furthermore, LD analysis identified 3 blocks of genotyped SNPs and 2 deleterious nsSNPs that may have damaging impact on protein function and thus could be employed for carrying genome-wide association studies. In conclusion, the information obtained in this study could be helpful for better understanding of regulatory roles of ATG5 and provides a base for its implication in population-based studies. ? 2016 Elsevier B.V.
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Keywords
Algorithm, Amino Acid Sequence Autophagy, Biodiversity, Computer Model, Correlation Coefficient, Gene, Gene Linkage Disequilibrium, Genotyping Technique, Human, Human Autophagy Related Gene 5, Mass Spectrometry, Nerve Degeneration, Phylogenetic Tree, Probability, Protein Interaction, Protein Processing, Protein Structure, Single Nucleotide Polymorphism
Citation
Vij, A., Randhawa, R., Parkash, J., & Changotra, H. (2016). Investigating regulatory signatures of human autophagy related gene 5 (ATG5) through functional in silico analysis. Meta Gene, 9, 237-248. doi: 10.1016/j.mgene.2016.07.012