Abstract
GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional maps of human tissues. The precise actions of genes are frequently dependent on their tissue context, yet direct assay of tissue-specific protein function and interactions remains infeasible in many normal human tissues and cell-types. With GIANT2, researchers can explore predicted tissue-specific functional roles of genes and reveal changes in those roles across tissues, all through interactive multi-network visualizations and analyses. Additionally, the NetWAS approach available through the server uses tissue-specific/cell-type networks predicted by GIANT2 to re-prioritize statistical associations from GWAS studies and identify disease-associated genes. GIANT2 predicts tissue-specific interactions by integrating diverse functional genomics data from now over 61 400 experiments for 283 diverse tissues and cell-types. GIANT2 does not require any registration or installation and is freely available for use at http://giant-v2.princeton.edu.
Highlights
Tissue and cell type specificity are critical aspects of complex human disease
Successful methods by us [10,11,12] and others [13,14] can integrate these functional genomics data to predict functional interactions in human, many of which are accessible through a web server [13,14,15]
Researchers can interact with GIANT by submitting individual genes or gene sets of interest for real-time integration of thousands of functional genomics experiments to predict tissue-specific interactions relevant to these genes and related processes
Summary
Tissue and cell type specificity are critical aspects of complex human disease. From impaired insulin signaling in diabetes [1,2] to neuronal loss in Parkinson’s disease [3,4,5], understanding tissue- and cell-lineage specific processes is necessary in elucidating disease pathophysiology and diseasegene relationships. Successful methods by us [10,11,12] and others [13,14] can integrate these functional genomics data to predict functional interactions in human, many of which are accessible through a web server [13,14,15]. GIANT (Genome-wide Analysis of gene Networks in Tissues), introduced in 2015 [16], is a prediction server for human tissue-specific gene interactions that enables biomedical researchers to interrogate tissue-specific action through multi-network visualizations and analyses.
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