ArticlePloS one2018
From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Method for the Dissection of Genomic Loci Associated with Chickpea Root Penetration Traits in Compact Soil.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Truncated variant rs373056577 confers increased risk of type 2 diabetes and missense variant rs121912717 is associated with hypertriglyceridemia in Bangladeshi population.Metabolism open · 2025Article
- Polygenic prediction of occupational status GWAS elucidates genetic and environmental interplay in intergenerational transmission, careers and health in UK Biobank.Nature human behaviour · 2025Article
- Molecular puzzle of insulin: structural assembly pathways and their role in diabetes.Frontiers in cell and developmental biology · 2025Review
- The NLRP3 inflammasome rs35829419 C>A polymorphism is associated with type 2 diabetes mellitus in Saudi Arabia.Saudi medical journal · 2023Article
- Molecular Genetics of Abnormal Redox Homeostasis in Type 2 Diabetes Mellitus.International journal of molecular sciences · 2023Review
- Type 2 diabetes mellitus and the risk of male infertility: a Mendelian randomization study.Frontiers in endocrinology · 2023Article
- Diabetes risk loci-associated pathways are shared across metabolic tissues.BMC genomics · 2022Article
- Genetic association between miR-27a and miR-449b polymorphisms and susceptibility to diabetes mellitus.Biomedical reports · 2022Article
- Nampt activator P7C3 ameliorates diabetes and improves skeletal muscle function modulating cell metabolism and lipid mediators.Journal of cachexia, sarcopenia and muscle · 2022Article
- Urgent need for consistent standards in functional enrichment analysis.PLoS computational biology · 2022Article
- Enlightening the molecular mechanisms of type 2 diabetes with a novel pathway clustering and pathway subnetwork approach.Turkish journal of biology = Turk biyoloji dergisi · 2022Article
- Mitochondrial haplogroups have a better correlation to insulin requirement than nuclear genetic variants for type 2 diabetes mellitus in Taiwanese individuals.Journal of diabetes investigation · 2022Article
- Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract.Indian journal of ophthalmology · 2021Article
- A resource to explore the discovery of rare diseases and their causative genes.Scientific data · 2021Article
- Epigenetic Regulation of β Cell Identity and Dysfunction.Frontiers in endocrinology · 2021Review
- CONQUER: an interactive toolbox to understand functional consequences of GWAS hits.NAR genomics and bioinformatics · 2020Article
- A selective inference approach for false discovery rate control using multiomics covariates yields insights into disease risk.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Most Important Thing We Give to People Is Hope: Overcoming Stigma in Diabetes and Obesity.Diabetes spectrum : a publication of the American Diabetes Association · 2020Article
- Association between rs2303861 polymorphism in CD82 gene and non-alcoholic fatty liver disease: a preliminary case-control study.Croatian medical journal · 2019Article
Corrections and comments
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Authors and funding
9 authors.
Funding
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Abstract
Genome-wide association studies (GWAS) have become a common method for discovery of gene-disease relationships, in particular for complex diseases like Type 2 Diabetes Mellitus (T2DM). The experience with GWAS analysis has revealed that the genetic risk for complex diseases involves cumulative, small effects of many genes and only some genes with a moderate effect. In order to explore the complexity of the relationships between T2DM genes and their potential function at the process level as effected by polymorphism effects, a secondary analysis of a GWAS meta-analysis is presented. Network analysis, pathway information and integration of different types of biological information such as eQTLs and gene-environment interactions are used to elucidate the biological context of the genetic variants and to perform an analysis based on data visualization. We selected a T2DM dataset from a GWAS meta-analysis, and extracted 1,971 SNPs associated with T2DM. We mapped 580 SNPs to 360 genes, and then selected 460 pathways containing these genes from the curated collection of WikiPathways. We then created and analyzed SNP-gene and SNP-gene-pathway network modules in Cytoscape. A focus on genes with robust connections to pathways permitted identification of many T2DM pertinent pathways. However, numerous genes lack literature evidence of association with T2DM. We also speculate on the genes in specific network structures obtained in the SNP-gene network, such as gene-SNP-gene modules. Finally, we selected genes relevant to T2DM from our SNP-gene-pathway network, using different sources that reveal gene-environment interactions and eQTLs. We confirmed functions relevant to T2DM for many genes and have identified some-LPL and APOB-that require further validation to clarify their involvement in T2DM.
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