anexVis: visual analytics framework for analysis of RNA expression

Summary: Although RNA expression data are accumulating at a remarkable speed, gaining insights from them still requires laborious analyses, which hinder many biological and biomedical researchers. This report introduces a visual analytics framework that applies several well‐known visualization techniques to leverage understanding of an RNA expression dataset. Our analyses on glycosaminoglycan‐related genes have demonstrated the broad application of this tool, anexVis (analysis of RNA expression), to advance the understanding of tissue‐specific glycosaminoglycan regulation and functions, and potentially other biological pathways. Availability and implementation: The application is accessible at https://anexvis.chpc.utah.edu/, source codes deposited on GitHub. Supplementary information: Supplementary data are available at Bioinformatics online.

[1]  J. Silbert,et al.  Biosynthesis of Chondroitin/Dermatan Sulfate , 2002, IUBMB life.

[2]  James R. Hennessy,et al.  shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics , 2017, bioRxiv.

[3]  Hudson H. Freeze,et al.  Genetic Disorders of Glycosylation , 2009 .

[4]  R. U. Margolis,et al.  Isolation and characterization of developmentally regulated chondroitin sulfate and chondroitin/keratan sulfate proteoglycans of brain identified with monoclonal antibodies. , 1991, The Journal of biological chemistry.

[5]  H. Kitagawa,et al.  Biosynthesis and function of chondroitin sulfate. , 2013, Biochimica et biophysica acta.

[6]  R. Frischknecht,et al.  Brevican: a key proteoglycan in the perisynaptic extracellular matrix of the brain. , 2012, The international journal of biochemistry & cell biology.

[7]  E. Wegman Hyperdimensional Data Analysis Using Parallel Coordinates , 1990 .

[8]  Jie Quan,et al.  QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization , 2015, BMC Genomics.

[9]  K Watanabe,et al.  Molecular cloning of brevican, a novel brain proteoglycan of the aggrecan/versican family. , 1994, The Journal of biological chemistry.

[10]  Piero Carninci,et al.  DEIVA: a web application for interactive visual analysis of differential gene expression profiles , 2017, BMC Genomics.

[11]  Johan Ledin,et al.  Heparan Sulfate Structure in Mice with Genetically Modified Heparan Sulfate Production* , 2004, Journal of Biological Chemistry.

[12]  Joseph Zaia,et al.  Organ-specific Heparan Sulfate Structural Phenotypes* , 2009, Journal of Biological Chemistry.

[13]  Rehan Akbani,et al.  A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data. , 2017, Cancer research.

[14]  Mary Goldman,et al.  Toil enables reproducible, open source, big biomedical data analyses , 2017, Nature Biotechnology.

[15]  William S York,et al.  Regulation of Glycan Structures in Animal Tissues , 2008, Journal of Biological Chemistry.

[16]  Dmitri D. Pervouchine,et al.  The human transcriptome across tissues and individuals , 2015, Science.

[17]  Renato V. Iozzo,et al.  Proteoglycan form and function: A comprehensive nomenclature of proteoglycans , 2015, Matrix biology : journal of the International Society for Matrix Biology.

[18]  Joseph Zaia,et al.  Mass spectral profiling of glycosaminoglycans from histological tissue surfaces. , 2013, Analytical chemistry.

[19]  Vincent Gardeux,et al.  ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data , 2016, bioRxiv.