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Gene. 2015 Dec 15;574(2):235-46. doi: 10.1016/j.gene.2015.08.012. Epub 2015 Aug 8.

Identification of hub glycogenes and their nsSNP analysis from mouse RNA-Seq data.

Author information

1
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.
2
Perdana University Centre for Bioinformatics, MARDI Complex, Jalan MAEPS Perdana, 43400 Serdang, Selangor, Malaysia. Electronic address: adeel@procarb.org.
3
Biomedical Informatics Center of ICMR, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
4
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.
5
School of Chemistry and Biochemistry, Thapar University, Patiala, Punjab 147004, India.

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.

KEYWORDS:

Glycogenes; Hubs; Interaction network; Secondary structure; Solvent accessibility; nsSNPs

PMID:
26260015
DOI:
10.1016/j.gene.2015.08.012
[Indexed for MEDLINE]

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