scholarly journals An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies

2017 ◽  
Vol 20 (3) ◽  
pp. 995-1003 ◽  
Author(s):  
Boyang Li ◽  
Qiongshi Lu ◽  
Hongyu Zhao
Keyword(s):  
Genome Annotation ◽  
Association Studies ◽  
Enrichment Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

Identification of Critical Core Genes of Sarcoma Based on Centrality Analysis of Networks Nodes

2020 ◽  
Vol 10 (7) ◽  
pp. 1776-1784
Author(s):  
Shudong Wang ◽  
Jixiao Wang ◽  
Xinzeng Wang ◽  
Yuanyuan Zhang ◽  
Tao Yi
Keyword(s):  
Association Studies ◽  
Meta Analysis ◽  
Complex Diseases ◽  
Enrichment Analysis ◽  
Gene Interaction ◽  
Core Gene ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Gene Set ◽  
Genome Wide

Genome-wide association studies (GWAS) are powerful tools for identifying pathogenic genes of complex diseases and revealing genetic structure of diseases. However, due to gene-to-gene interactions, only a part of the hereditary factors can be revealed. The meta-analysis based on GWAS can integrate gene expression data at multiple levels and reveal the complex relationship between genes. Therefore, we used meta-analysis to integrate GWAS data of sarcoma to establish complex networks and discuss their significant genes. Firstly, we established gene interaction networks based on the data of different subtypes of sarcoma to analyze the node centralities of genes. Secondly, we calculated the significant score of each gene according to the Staged Significant Gene Network Algorithm (SSGNA). Then, we obtained the critical gene set HYC of sarcoma by ranking the scores, and then combined Gene Ontology enrichment analysis and protein network analysis to further screen it. Finally, the critical core gene set Hcore containing 47 genes was obtained and validated by GEPIA analysis. Our method has certain generalization performance to the study of complex diseases with prior knowledge and it is a useful supplement to genome-wide association studies.

scholarly journals INRICH: interval-based enrichment analysis for genome-wide association studies

2012 ◽  
Vol 28 (13) ◽  
pp. 1797-1799 ◽  
Author(s):  
Phil H. Lee ◽  
Colm O'Dushlaine ◽  
Brett Thomas ◽  
Shaun M. Purcell
Keyword(s):  
Association Studies ◽  
Enrichment Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals SNP-based pathway enrichment analysis for genome-wide association studies

2011 ◽  
Vol 12 (1) ◽  
pp. 99 ◽  
Author(s):  
Lingjie Weng ◽  
Fabio Macciardi ◽  
Aravind Subramanian ◽  
Guia Guffanti ◽  
Steven G Potkin ◽  
...  
Keyword(s):  
Association Studies ◽  
Enrichment Analysis ◽  
Genome Wide Association ◽  
Pathway Enrichment Analysis ◽  
Genome Wide Association Studies ◽  
Pathway Enrichment ◽  
Genome Wide

scholarly journals Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies

2021 ◽  
Vol 12 ◽  
Author(s):  
Michal Marczyk ◽  
Agnieszka Macioszek ◽  
Joanna Tobiasz ◽  
Joanna Polanska ◽  
Joanna Zyla
Keyword(s):  
Association Studies ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Gene Set Analysis ◽  
Genome Wide Association Studies ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Genome Wide ◽  
The Impact

A typical genome-wide association study (GWAS) analyzes millions of single-nucleotide polymorphisms (SNPs), several of which are in a region of the same gene. To conduct gene set analysis (GSA), information from SNPs needs to be unified at the gene level. A widely used practice is to use only the most relevant SNP per gene; however, there are other methods of integration that could be applied here. Also, the problem of nonrandom association of alleles at two or more loci is often neglected. Here, we tested the impact of incorporation of different integrations and linkage disequilibrium (LD) correction on the performance of several GSA methods. Matched normal and breast cancer samples from The Cancer Genome Atlas database were used to evaluate the performance of six GSA algorithms: Coincident Extreme Ranks in Numerical Observations (CERNO), Gene Set Enrichment Analysis (GSEA), GSEA-SNP, improved GSEA for GWAS (i-GSEA4GWAS), Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA), and Over-Representation Analysis (ORA). Association of SNPs to phenotype was calculated using modified McNemar’s test. Results for SNPs mapped to the same gene were integrated using Fisher and Stouffer methods and compared with the minimum p-value method. Four common measures were used to quantify the performance of all combinations of methods. Results of GSA analysis on GWAS were compared to the one performed on gene expression data. Comparing all evaluation metrics across different GSA algorithms, integrations, and LD correction, we highlighted CERNO, and MAGENTA with Stouffer as the most efficient. Applying LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. When Fisher or Stouffer were used with LD, sensitivity and reproducibility were also better. Using any integration method was beneficial in comparison with a minimum p-value method in specific combinations. The correlation between GSA results from genomic and transcriptomic level was the highest when Stouffer integration was combined with LD correction. We thoroughly evaluated different approaches to GSA in GWAS in terms of performance to guide others to select the most effective combinations. We showed that LD correction and Stouffer integration could increase the performance of enrichment analysis and encourage the usage of these techniques.

scholarly journals Variable set enrichment analysis in genome-wide association studies

2011 ◽  
Vol 19 (8) ◽  
pp. 893-900 ◽  
Author(s):  
Wei Yang ◽  
Lisa de las Fuentes ◽  
Victor G Dávila-Román ◽  
C Charles Gu
Keyword(s):  
Association Studies ◽  
Enrichment Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals haploR: an R package for querying web-based annotation tools

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 97 ◽  
Author(s):  
Ilya Y. Zhbannikov ◽  
Konstantin Arbeev ◽  
Svetlana Ukraintseva ◽  
Anatoliy I. Yashin
Keyword(s):  
Genome Annotation ◽  
Association Studies ◽  
R Package ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genetic Associations ◽  
Data Frame ◽  
Web Based ◽  
Genome Wide

We developed haploR, an R package for querying web based genome annotation tools HaploReg and RegulomeDB. haploR gathers information in a data frame which is suitable for downstream bioinformatic analyses. This will facilitate post-genome wide association studies streamline analysis for rapid discovery and interpretation of genetic associations.

scholarly journals Expression Sensitivity Analysis of Human Disease Related Genes

2013 ◽  
Vol 2013 ◽  
pp. 1-8
Author(s):  
Liang-Xiao Ma ◽  
Ya-Jun Wang ◽  
Jing-Fang Wang ◽  
Xuan Li ◽  
Pei Hao
Keyword(s):  
Profile Analysis ◽  
Association Studies ◽  
Enrichment Analysis ◽  
Genome Wide Association ◽  
Disease Genes ◽  
Genome Wide Association Studies ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Disease Related Genes ◽  
Essential Function

Background. Genome-wide association studies (GWAS) have shown its revolutionary power in seeking the influenced loci on complex diseases genetically. Thousands of replicated loci for common traits are helpful in diseases risk assessment. However it is still difficult to elucidate the variations in these loci that directly cause susceptibility to diseases by disrupting the expression or function of a protein currently.Results. We evaluate the expression features of disease related genes and find that different diseases related genes show different expression perturbation sensitivities in various conditions. It is worth noting that the expression of some robust disease-genes doesn’t show significant change in their corresponding diseases, these genes might be easily ignored in the expression profile analysis.Conclusion. Gene ontology enrichment analysis indicates that robust disease-genes execute essential function in comparison with sensitive disease-genes. The diseases associated with robust genes seem to be relatively lethal like cancer and aging. On the other hand, the diseases associated with sensitive genes are apparently nonlethal like psych and chemical dependency diseases.

scholarly journals Identifying insomnia-related chemicals through integrative analysis of genome-wide association studies and chemical–genes interaction information

SLEEP ◽  
2020 ◽  
Vol 43 (9) ◽  
Author(s):  
Om Prakash Kafle ◽  
Shiqiang Cheng ◽  
Mei Ma ◽  
Ping Li ◽  
Bolun Cheng ◽  
...  
Keyword(s):  
Association Studies ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Modern Society ◽  
Environmental Chemicals ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Study Results

Abstract Study Objectives Insomnia is a common sleep disorder and constitutes a major issue in modern society. We provide new clues for revealing the association between environmental chemicals and insomnia. Methods Three genome-wide association studies (GWAS) summary datasets of insomnia (n = 113,006, n = 1,331,010, and n = 453,379, respectively) were driven from the UK Biobank, 23andMe, and deCODE. The chemical–gene interaction dataset was downloaded from the Comparative Toxicogenomics Database. First, we conducted a meta-analysis of the three datasets of insomnia using the METAL software. Using the result of meta-analysis, transcriptome-wide association studies were performed to calculate the expression association testing statistics of insomnia. Then chemical-related gene set enrichment analysis (GSEA) was used to explore the association between chemicals and insomnia. Results For GWAS meta-analysis dataset of insomnia, we identified 42 chemicals associated with insomnia in brain tissue (p < 0.05) by GSEA. We detected five important chemicals such as pinosylvin (p = 0.0128), bromobenzene (p = 0.0134), clonidine (p = 0.0372), gabapentin (p = 0.0372), and melatonin (p = 0.0404) which are directly associated with insomnia. Conclusion Our study results provide new clues for revealing the roles of environmental chemicals in the development of insomnia.

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