A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

Epigenome-wide association study of DNA methylation in panic disorder

(2017) Mihoko Shimada-Sugimoto et al.   Clinical Epigenetics

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Gene set analysis: A step-by-step guide

(2015) Michael A. Mooney et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

WikiPathways: capturing the full diversity of pathway knowledge

(2015) Martina Kutmon et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

PathVisio 3: An Extendable Pathway Analysis Toolbox

(2015) Martina Kutmon et al.   PLoS Computational Biology

Characterizing gene-gene interactions in a statistical epistasis network of twelve candidate genes for obesity

(2015) Rishika De et al.   BioData Mining

Pathway Analysis: State of the Art

(2015) Miguel A. García-Campos et al.   Frontiers in Physiology

Data integration in the era of omics: current and future challenges

(2014) David Gomez-Cabrero et al.   BMC Systems Biology

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Detecting epistasis in human complex traits

(2014) Wen-Hua Wei et al.   NATURE REVIEWS GENETICS

Genome-wide pathway analysis of breast cancer

(2014) Young Ho Lee et al.   TUMOR BIOLOGY

CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits

(2014) Laurence D Parnell et al.   BioData Mining

Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement

(2013) David Moher   ANNALS OF INTERNAL MEDICINE

enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets

(2013) Christian Partl et al.   BMC BIOINFORMATICS

Pathway-Based Approaches for Sequencing-Based Genome-Wide Association Studies

(2013) Guodong Wu et al.   GENETIC EPIDEMIOLOGY

Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets

(2013) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Integrative pathway analysis of a genome-wide association study of V̇o2max response to exercise training

(2013) Sujoy Ghosh et al.   JOURNAL OF APPLIED PHYSIOLOGY

Bringing genome-wide association findings into clinical use

(2013) Teri A. Manolio   NATURE REVIEWS GENETICS

Simultaneous Identification of Multiple Driver Pathways in Cancer

(2013) Mark D. M. Leiserson et al.   PLoS Computational Biology

Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer

(2012) Peilin Jia et al.   BMC Systems Biology

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization

(2012) A. Lex et al.   COMPUTER GRAPHICS FORUM

Pathway analysis of genome-wide association studies for Parkinson’s disease

(2012) Gwan Gyu Song et al.   MOLECULAR BIOLOGY REPORTS

Comparison of Pathway Analysis Approaches Using Lung Cancer GWAS Data Sets

(2012) Gordon Fehringer et al.   PLoS One

Comparison of Methods for Competitive Tests of Pathway Analysis

(2012) Marina Evangelou et al.   PLoS One

Characterizing genetic interactions in human disease association studies using statistical epistasis networks

(2011) Ting Hu et al.   BMC BIOINFORMATICS

Knowledge management for Systems Biology a general and visually driven framework applied to translational medicine

(2011) Dieter Maier et al.   BMC Systems Biology

What should the genome-wide significance threshold be? Empirical replication of borderline genetic associations

(2011) Orestis A Panagiotou et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies

(2010) Hua Zhong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pathway analysis of gene lists associated with platinum-based chemotherapy resistance in ovarian cancer: The big picture

(2010) Jozien Helleman et al.   GYNECOLOGIC ONCOLOGY

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

(2010) Florian Markowetz   PLoS Computational Biology

Path: a tool to facilitate pathway-based genetic association analysis

(2009) D. Zamar et al.   BIOINFORMATICS

Pathway analysis by adaptive combination ofP-values

(2009) Kai Yu et al.   GENETIC EPIDEMIOLOGY

Analyses of associations with asthma in four asthma population samples from Canada and Australia

(2009) Denise Daley et al.   HUMAN GENETICS

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Molecular population genetics of PCSK9: a signature of recent positive selection

(2008) Keyue Ding et al.   Pharmacogenetics and Genomics

Pathway-based association analysis of genome-wide screening data suggest that genes associated with the ??-aminobutyric acid receptor signaling pathway are involved in neuroleptic-induced, treatment-resistant tardive dyskinesia

(2008) Toshiya Inada et al.   Pharmacogenetics and Genomics