scholarly journals In silico analysis of non-synonymous single nucleotide polymorphisms of human DEFB1 gene

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Harini Venkata Subbiah ◽  
Polani Ramesh Babu ◽  
Usha Subbiah
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
In Silico ◽  
In Silico Analysis ◽  
Gene Interaction ◽  
Nucleotide Polymorphisms ◽  
Amino Acid Residues ◽  
Single Nucleotide ◽  
Project Hope ◽  
The Impact ◽  
Structure And Functions

Abstract Background Single nucleotide polymorphisms (SNPs) play a significant role in differences in individual’s susceptibility to diseases, and it is imperative to differentiate potentially harmful SNPs from neutral ones. Defensins are small cationic antimicrobial peptides that serve as antimicrobial and immunomodulatory molecules, and SNPs in β-defensin 1 (DEFB1 gene) have been associated with several diseases. In this study, we have determined deleterious SNPs of the DEFB1 gene that can affect the susceptibility to diseases by using different computational methods. Non-synonymous SNPs (nsSNPs) of the DEFB1 gene that have the ability to affect protein structure and functions were determined by several in silico tools—SIFT, PolyPhen v2, PROVEAN, SNAP, PhD-SNP, and SNPs&GO. Then, nsSNPs identified to be potentially deleterious were further analyzed by I-Mutant and ConSurf. Post-translational modifications mediated by nsSNPs were predicted by ModPred, and gene-gene interaction was studied by GeneMANIA. Finally, nsSNPs were submitted to Project HOPE analysis. Results Ten nsSNPs of the DEFB1 gene were found to be potentially deleterious: rs1800968, rs55874920, rs56270143, rs140503947, rs145468425, rs146603349, rs199581284, rs201260899, rs371897938, rs376876621. I-Mutant server showed that nsSNPs rs140503947 and rs146603349 decreased stability of the protein, and ConSurf analysis revealed that SNPs were located in conserved regions. The physiochemical properties of the polymorphic amino acid residues and their effect on structure were determined by Project HOPE. Conclusion This study has determined high-risk deleterious nsSNPs of β-defensin 1 and could increase the knowledge of nsSNPs towards the impact of mutations on structure and functions mediated by β-defensin 1 protein.

scholarly journals Single nucleotide polymorphisms in the ANGPTL4 gene and the SNP-SNP interactions on the risk of atherosclerotic Ischaemic stroke

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chaoxiong Shen ◽  
Daofeng Fan ◽  
Huajun Fu ◽  
Chong Zheng ◽  
Yinjuan Chen ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Single Nucleotide Polymorphisms ◽  
Gene Interaction ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Testing Accuracy ◽  
Medical University ◽  
The Impact ◽  
Snp Interaction ◽  
Control Study

Abstract Objectives The purpose of this study was to investigate the impact of single nucleotide polymorphisms (SNPs) in the ANGPTL4 gene and the SNP–SNP interactions on atherosclerotic ischemic stroke (IS) risk. Patients and methods A case-control study was conducted. A total of 360 patients with atherosclerotic IS and 342 controls between December 2018 and December 2019 from Longyan First Hospital affiliated to Fujian Medical University were included. A logistic regression model was used to examine the association between SNPs and atherosclerotic IS risk. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. Generalized multifactor dimensionality reduction was employed to analyze the SNP-SNP interaction. Results Logistic regression analysis showed that atherosclerotic IS risk was significantly lower in carriers with the rs11672433-T allele than those with the CC genotype (CT+ TT vs. CC); adjusted OR, 0.005; 95% CI, 0.02–0.11. We found a significant 2-locus model (P = 0.0010) involving rs11672433 and rs4076317; the cross-validation consistency of this model was 10 of 10, and the testing accuracy was 57.96%. Participants with the CT or TT of rs11672433 and CC of rs4076317 genotype have the lowest atherosclerotic IS risk, compared to subjects with CC of rs11672433 and the CC of rs4076317 genotype, OR (95%CI) was 0.06(0.02–0.22), after covariates adjustment for gender, age, smoking and alcohol status, hypertension, Diabetes mellitus, TG, TC, HDL-C, LDL-C, Uric acid. Conclusions We found that rs11672433 was associated with decreased atherosclerotic IS risk; we also found that gene–gene interaction between rs11672433 and rs4076317 was associated with decreased atherosclerotic IS risk.

scholarly journals In Silico Analysis of Single Nucleotide Polymorphisms (SNPs) in Human <i>MPL</i> Gene

2019 ◽  
Vol 7 (4) ◽  
pp. 124
Author(s):  
Mohamed Mubarak Babeker ◽  
Afra Mohamed Suliman Albakry ◽  
Mohammed Nagm Eldin Elsamani ◽  
Gihan Mossalami ◽  
Hind Abdelaziz Elnasri ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
In Silico ◽  
In Silico Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Silico Analysis

scholarly journals In silico analysis of single nucleotide polymorphisms (SNPs) in human FOXC2 gene

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 243
Author(s):  
Mohammed Nimir ◽  
Mohanad Abdelrahim ◽  
Mohamed Abdelrahim ◽  
Mahil Abdalla ◽  
Wala eldin Ahmed ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Conservation Score ◽  
Interaction Network ◽  
In Silico Analysis ◽  
Gene Interaction ◽  
Nucleotide Polymorphisms ◽  
Gene Interaction Network ◽  
Single Nucleotide ◽  
Functional Studies ◽  
Advantages And Disadvantages

Introduction: Lymphedema is an abnormal accumulation of interstitial fluid, due to inefficient uptake and reduced flow, leading to swelling and disability, mostly in the extremities. Hereditary lymphedema usually occurs as an autosomal dominant trait with allelic heterogeneity. Methods: We identified single nucleotide polymorphisms (SNPs) in the FOXC2 gene using dbSNP, analyzed their effect on the resulting protein using VEP and Biomart, modelled the resulting protein using Project HOPE, identified gene – gene interactions using GeneMANIA and predicted miRNAs affected and the resulting effects of SNPs in the 5’ and 3’ regions using PolymiRTS. Results: We identified 473 SNPs - 429 were nsSNPs and 44 SNPs were in the 5’ and 3’ UTRs. In total, 2 SNPs - rs121909106 and rs121909107 - have deleterious effects on the resulting protein, and a 3D model confirmed those effects. The gene – gene interaction network showed the involvement of FOXC2 protein in the development of the lymphatic system. hsa-miR-6886-5p, hsa-miRS-6886-5p, hsa-miR-6720-3p, which were affected by the SNPs rs201118690, rs6413505, rs201914560, respectively, were the most important miRNAs affected, due to their high conservation score. Conclusions: rs121909106 and rs121909107 were predicted to have the most harmful effects, while hsa-miR-6886-5p, hsa-miR-6886-5p and hsa-miR-6720-3p were predicted to be the most important miRNAs affected. Computational biology tools have advantages and disadvantages, and the results they provide are predictions that require confirmation using methods such as functional studies.

In silico analysis of Single Nucleotide Polymorphisms (SNPs) in human BRAF gene

Gene ◽  
2012 ◽  
Vol 508 (2) ◽  
pp. 188-196 ◽  
Author(s):  
Muhammad Ramzan Manwar Hussain ◽  
Noor Ahmad Shaik ◽  
Jumana Yousuf Al-Aama ◽  
Hani Z. Asfour ◽  
Fatima Subhani Khan ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
In Silico ◽  
In Silico Analysis ◽  
Nucleotide Polymorphisms ◽  
Braf Gene ◽  
Single Nucleotide ◽  
Silico Analysis
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