title: Identification of hub glycogenes and their nsSNP analysis from mouse RNA-Seq data.
abstract: Glycogenes regulate a large number of biological processes such as cancer and development. In this work, we created an interaction network of 923 glycogenes to detect potential hubs from different mouse tissues using RNA-Seq data. DAVID functional cluster analysis revealed enrichment of immune response, glycoprotein and cholesterol metabolic processes. We also explored nsSNPs that may modify the expression and function of identified hubs using computational methods. We observe that the number of nsSNPs predicted by any two methods to affect protein function is 4, 7 and 2 for FLT1, NID2 and TNFRSF1B. Residues in the native and mutant proteins were analyzed for solvent accessibility and secondary structure change. Analysis of hubs can help in determining their degree of conservation and understanding their functions in biological processes. The nsSNPs proposed in this work may be further targeted through experimental methods for understanding structural and functional relationships of hub mutants.
authors.affiliation: School of Chemistry and Biochemistry, Thapar University, Patiala, Punjab 147004, India; Biomedical Informatics Center of ICMR, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India. Electronic address: ahmadfirozbin@gmail.com.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Firoz
authors.affiliation: Perdana University Centre for Bioinformatics, MARDI Complex, Jalan MAEPS Perdana, 43400 Serdang, Selangor, Malaysia. Electronic address: adeel@procarb.org.
authors.forename: Adeel
authors.initials: A
authors.lastname: Malik
authors.affiliation: Biomedical Informatics Center of ICMR, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
authors.forename: Sanjay Kumar
authors.initials: SK
authors.lastname: Singh
authors.affiliation: Biomedical Informatics Center of ICMR, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India; Department of Nephrology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
authors.forename: Vivekanand
authors.initials: V
authors.lastname: Jha
authors.affiliation: School of Chemistry and Biochemistry, Thapar University, Patiala, Punjab 147004, India.
authors.forename: Amjad
authors.initials: A
authors.lastname: Ali
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D006023:Glycoproteins / Q000737:chemistry / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D051379:Mice; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D017433:Protein Structure, Secondary; D017423:Sequence Analysis, RNA
chemical_list: D006023:Glycoproteins
keywords: Glycogenes; Hubs; Interaction network; Secondary structure; Solvent accessibility; nsSNPs