SNPStats: a web tool for the analysis of association studies

Solé, Xavier; Guinó, Elisabet; Valls, Joan; Iniesta, Raquel; Moreno, Vı́ctor

doi:10.1093/bioinformatics/btl268

Cited by 1,728 publications

(1,144 citation statements)

References 4 publications

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“…51 The association between genetic and microbiological data was tested by logistic regression and CochraneArmitage interaction in the trend analysis using the SNPStats web-based tool. 52 A P-value < 0.05 was considered statistically significant.…”

Section: Discussionmentioning

confidence: 99%

TBX21-1993T/C (rs4794067) polymorphism is associated with increased risk of chronic periodontitis and increased T-bet expression in periodontal lesions, but does not significantly impact the IFN-g transcriptional level or the pattern of periodontophatic bacterial infection

et al. 2015

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Section: Discussionmentioning

confidence: 99%

TBX21-1993T/C (rs4794067) polymorphism is associated with increased risk of chronic periodontitis and increased T-bet expression in periodontal lesions, but does not significantly impact the IFN-g transcriptional level or the pattern of periodontophatic bacterial infection

et al. 2015

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“…p<0.05 was defined as a threshold for significant changes. SNPs association analysis was performed with SNPStats [20]; http://bioinfo.iconcologia. net/snpstats/start.htm].…”

Section: Discussionmentioning

confidence: 99%

Expression and potential role of apolipoprotein D on the death–survival balance of human colorectal cancer cells under oxidative stress conditions

Bajo‐Grañeras

Crespo‐Sanjuán

García-Centeno

et al. 2013

Int J Colorectal Dis

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“…All statistical analyses were performed using the PASW (v. 18.0 for WINDOWS, Chicago), except for statistical power, which we calculated with the StatMate software, version 2.0 (GraphPad, San Diego, CA, USA) and analysis of haplotypes, which was performed using the free Web-based application SNPStats (Sole et al 2006). Haplotype frequencies were estimated using the implementations of the EM algorithm coded into the haplo.stats package.…”

Section: Methodsmentioning

confidence: 99%

FNDC5 (irisin) gene and exceptional longevity: a functional replication study with rs16835198 and rs726344 SNPs

Sanchís-Gomar

Garatachea

et al. 2014

AGE

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Irisin might play an important role in reducing the risk of obesity, insulin resistance, or several related diseases, and high irisin levels may contribute to successful aging. Thus, the irisin precursor (FNDC5) gene is a candidate to influence exceptional longevity (EL), i.e., being a centenarian. It has been recently shown that two single-nucleotide polymorphisms (SNPs) in the FNDC5 gene, rs16835198 and rs726344, are associated with in vivo insulin sensitivity in adults. We determined luciferase gene reporter AGE (2014) 36:9733 DOI 10.1007 Fabian Sanchis-Gomar and Nuria Garatachea contributed equally to this paper activity in the two above-mentioned SNPs and studied genotype distributions among centenarians (n=175, 144 women) and healthy controls (n=347, 142 women) from Spain. We also studied an Italian [79 healthy centenarians (40 women) and 316 healthy controls (156 women)] and a Japanese cohort [742 centenarians (623 women) and 499 healthy controls (356 women)]. The rs726344 SNP had functional significance, as shown by differences in luciferase activity between the constructs of this SNP (all P≤0.05), with the variant A-allele having higher luciferase activity compared with the G-allele (P = 0.04). For the rs16835198 SNP, the variant T-allele tended to show higher luciferase activity compared with the G-allele (P=0.07). However, we found no differences between genotype/allele frequencies of the two SNPs in centenarians versus controls in any cohort, and no significant association (using logistic regression adjusted by sex) between the two SNPs and EL. Further research is needed with different cohorts as well as with additional variants in the FNDC5 gene or in other genes involved in irisin signaling.

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SNPStats: a web tool for the analysis of association studies

Abstract: http://bioinfo.iconcologia.net/SNPstats. Source code for local installation is available under GNU license.

Cited by 1,728 publications

References 4 publications

TBX21-1993T/C (rs4794067) polymorphism is associated with increased risk of chronic periodontitis and increased T-bet expression in periodontal lesions, but does not significantly impact the IFN-g transcriptional level or the pattern of periodontophatic bacterial infection

TBX21-1993T/C (rs4794067) polymorphism is associated with increased risk of chronic periodontitis and increased T-bet expression in periodontal lesions, but does not significantly impact the IFN-g transcriptional level or the pattern of periodontophatic bacterial infection

Expression and potential role of apolipoprotein D on the death–survival balance of human colorectal cancer cells under oxidative stress conditions

FNDC5 (irisin) gene and exceptional longevity: a functional replication study with rs16835198 and rs726344 SNPs

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