University of Khartoum

In Silico Analysis of Single Nucleotide Polymorphisms (Snps) In Human FOXC2 Gene [Version 1; Referees: Awaiting Peer Review]

In Silico Analysis of Single Nucleotide Polymorphisms (Snps) In Human FOXC2 Gene [Version 1; Referees: Awaiting Peer Review]

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dc.contributor.author Nimir, Mohammed
dc.contributor.author Abdelrahim, Mohanad
dc.contributor.author Abdelrahim, Mohamed
dc.contributor.author Abdalla, Mahil
dc.contributor.author Ahmed, Walaeldin
dc.contributor.author Abdullah, Muhanned
dc.contributor.author Abdelhamid, Muzamil Mahdi
dc.contributor.other Parasitology and Medical Entomology en_US
dc.date 2017-03
dc.date.accessioned 2017-05-30T09:00:23Z
dc.date.available 2017-05-30T09:00:23Z
dc.date.submitted 2017
dc.identifier.uri http://khartoumspace.uofk.edu/123456789/25105
dc.description.abstract Introduction: Lymphedema is 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 448 SNPs - 429 were nsSNPs and 44 SNPs were in the 5’ and 3’ UTRs. In total, 2 SNPs 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. en_US
dc.language.iso en en_US
dc.publisher University of Khartoum en_US
dc.subject Bioinformatics; FOXC2; In silico; Primary lymphedema; SNP; miRNA en_US
dc.title In Silico Analysis of Single Nucleotide Polymorphisms (Snps) In Human FOXC2 Gene [Version 1; Referees: Awaiting Peer Review] en_US
dc.type Publication en_US
dc.Faculty Endemic Diseases en_US

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