Journal ArticleDOI
Applications of computational algorithm tools to identify functional SNPs
C. George Priya Doss,C. Sudandiradoss,R. Rajasekaran,Parikshit Choudhury,Priyanka Sinha,Pragnya Hota,Udit Prakash Batra,Sethumadhavan Rao +7 more
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TLDR
This work analyzed the SNPs that can alter the expression and function of transcriptional factor TP53 as a pipeline and proposed modeled structure for the mutant proteins and compared them with the native protein.Abstract:
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variations in humans Understanding the functions of SNPs can greatly help to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases The method to identify functional SNPs from a pool, containing both functional and neutral SNPs is challenging by experimental protocols To explore possible relationships between genetic mutation and phenotypic variation, different computational algorithm tools like Sorting Intolerant from Tolerant, Polymorphism Phenotyping, UTRscan, FASTSNP, and PupaSuite were used for prioritization of high-risk SNPs in coding region (exonic nonsynonymous SNPs) and noncoding regions (intronic and exonic 5' and 3'-untranslated region (UTR) SNPs) In this work, we have analyzed the SNPs that can alter the expression and function of transcriptional factor TP53 as a pipeline and for providing a guide to experimental work We identified the possible mutations and proposed modeled structure for the mutant proteins and compared them with the native protein These nsSNPs play a critical role in cancer association studies aiming to explain the disparity in cancer treatment responses as well as to improve the effectiveness of the cancer treatments Our results endorse the study with in vivo experimental protocolsread more
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Advances in translational bioinformatics: computational approaches for the hunting of disease genes
TL;DR: This review highlights the latest advances in the field of translational bioinformatics, focusing on the advances of computational techniques to search for and classify disease genes.
Journal ArticleDOI
Single nucleotide polymorphisms of Toll-like receptor 4 decrease the risk of development of hepatocellular carcinoma.
Shi Minmin,Xu Xiaoqian,Chen Hao,Chen Hao,Shen Baiyong,Shen Baiyong,Deng Xiaxing,Deng Xiaxing,Xie Junjie,Zhan Xi,Zhao Jianquan,Jiang Songyao +11 more
TL;DR: It is suggested that the risk of hepatocellular carcinoma was associated with TLR4 sequence variation, and single nucleotide polymorphisms ofTLR4 may play an important protective role in the development of liver cancer.
Journal ArticleDOI
Toll-Like Receptor (TLR2 and TLR4) Polymorphisms and Chronic Obstructive Pulmonary Disease
Simona E. Budulac,H. Marike Boezen,Pieter S. Hiemstra,Thérèse S. Lapperre,Judith M. Vonk,Wim Timens,Dirkje S. Postma +6 more
TL;DR: This is the first longitudinal study showing that tagging SNPs in TLR2 and TLR4 are associated with the level and decline of lung function as well as with inflammatory cell numbers in induced sputum in COPD patients, suggesting a role in the severity and progression of COPD.
Journal ArticleDOI
A Comprehensive In Silico Analysis of the Functional and Structural Impact of SNPs in the IGF1R Gene
TL;DR: A comprehensive analysis of the functional and structural impact of all known SNPs in this gene using publicly available computational prediction tools shows that a mutation from arginine to cysteine at position 1216 on the surface of the protein caused the greatest impact on stability.
Journal ArticleDOI
Genetic variations in TERT-CLPTM1L locus are associated with risk of lung cancer in Chinese population.
Rong Zhong,Li Liu,Li Zou,Yaowu Zhu,Wei Chen,Beibei Zhu,Na Shen,Rui Rui,Lu Long,Juntao Ke,Xuzai Lu,Ti Zhang,Yu Zhang,Zhenling Wang,Lifeng Liu,Yu Sun,Liming Cheng,Xiaoping Miao +17 more
TL;DR: Findings indicated that the function‐validated and potentially functional variations in TERT‐CLPTM1L locus, modified by smoking, may play a substantial role in the susceptibility to lung cancer.
References
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Journal ArticleDOI
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002.
Graziano Pesole,Sabino Liuni,Giorgio Grillo,Flavio Licciulli,Flavio Mignone,Carmela Gissi,Cecilia Saccone +6 more
TL;DR: UTRdb, a specialized database of 5' and 3' untranslated sequences of eukaryotic mRNAs cleaned from redundancy is developed, enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role.
Journal ArticleDOI
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
TL;DR: The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures.
Journal ArticleDOI
Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput.
TL;DR: A general description of SNP typing protocols and a summary of current methods for each step of the protocol are pointed out, pointing out the unique features and weaknesses of these techniques as well as comparing the cost and throughput structures of the technologies.
Human molecular genetics 3
TL;DR: Human molecular genetics 3, Human molecular genetics as discussed by the authors, Human Molecular Genetics 3, مرکز فناوری اطلاعات, اراع رسانی, اةشا-ورزی
Journal ArticleDOI
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes
Lucia Conde,Juan M. Vaquerizas,Carles Ferrer-Costa,Xavier de la Cruz,Modesto Orozco,Joaquín Dopazo +5 more
TL;DR: PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level and will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease.