SysMyo: tailored bioinformatics tools for omics data exploration in muscular dystrophy and other neuromuscular disorders

Matthew Thorley, Apostolos Malatras, Emilia Maria Cristina Mazza, L Zhu, Stephanie Duguez, William Duddy

Research output: Contribution to conferenceAbstract

Abstract

Background: Most bioinformatics tools and data resources are designed to have wide application, whereas more tailored tools can provide analyses that are adapted to specifi c pathologies or tissue types.
Aims: Here we introduce systems biology tools adapted to myology research, currently or soon-to-be accessible through the Sys-Myo web portal (http://sysmyo.rhcloud.com/).
Methods: Data are derived from (i) public resources — Gene Expression Omnibus, The Gene Ontology, Uniprot, Mentha, IntAct, GeneMANIA — and (ii) SILAC proteomics combined with immuno pull-down of the Dystrophin protein and its binding partners. Data are collated and analyzed using programmatic tools such as R/Bioconductor and made accessible through a website hosted on the RedHat OpenShift cloud platform.
Results: Four tools are introduced. (i) When given a list of genes/proteins, CellWhere returns a network map of gene functional associations overlaid onto a schema of the cell and its subcellular compartments. The tool can be used to screen data for proteins that may be at strongly muscle-relevant cell compartments. (ii) Public transcriptomic data are used to create the Muscle Gene Sets resource, which provides lists of genes that were diff erentially expressed across muscle studies, and can be used for functional enrichment testing. (iii) The Dystrophin Interactome tool combines public functional association data with new SILAC experimental data on the binding partners of the Dystrophin protein, enabling exploration of the functional interactions of this important muscle protein. (iv) MyoMiner will summarize gene co-expression across previous microarray studies of muscle tissues and pathologies, potentially yielding a new empirically-derived defi nition of functional gene clusters in muscle.
Conclusions: the Sys-Myo portal off ers publicly accessible tools of potential use to researchers in neuromuscular disease.
LanguageEnglish
PagesS8
Number of pages1
DOIs
Publication statusPublished - 1 Mar 2017

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Muscular Dystrophies
Computational Biology
Dystrophin
Muscles
Pathology
Mentha
Gene Expression
Neuromuscular Diseases
Gene Ontology
Proteins
Systems Biology
Muscle Proteins
Gene Regulatory Networks
Multigene Family
Protein Binding
Proteomics
Muscle Cells
Genes
Research Personnel
Research

Cite this

@conference{d3587b5286f849d0a6b3f94fcf077be3,
title = "SysMyo: tailored bioinformatics tools for omics data exploration in muscular dystrophy and other neuromuscular disorders",
abstract = "Background: Most bioinformatics tools and data resources are designed to have wide application, whereas more tailored tools can provide analyses that are adapted to specifi c pathologies or tissue types.Aims: Here we introduce systems biology tools adapted to myology research, currently or soon-to-be accessible through the Sys-Myo web portal (http://sysmyo.rhcloud.com/).Methods: Data are derived from (i) public resources — Gene Expression Omnibus, The Gene Ontology, Uniprot, Mentha, IntAct, GeneMANIA — and (ii) SILAC proteomics combined with immuno pull-down of the Dystrophin protein and its binding partners. Data are collated and analyzed using programmatic tools such as R/Bioconductor and made accessible through a website hosted on the RedHat OpenShift cloud platform. Results: Four tools are introduced. (i) When given a list of genes/proteins, CellWhere returns a network map of gene functional associations overlaid onto a schema of the cell and its subcellular compartments. The tool can be used to screen data for proteins that may be at strongly muscle-relevant cell compartments. (ii) Public transcriptomic data are used to create the Muscle Gene Sets resource, which provides lists of genes that were diff erentially expressed across muscle studies, and can be used for functional enrichment testing. (iii) The Dystrophin Interactome tool combines public functional association data with new SILAC experimental data on the binding partners of the Dystrophin protein, enabling exploration of the functional interactions of this important muscle protein. (iv) MyoMiner will summarize gene co-expression across previous microarray studies of muscle tissues and pathologies, potentially yielding a new empirically-derived defi nition of functional gene clusters in muscle.Conclusions: the Sys-Myo portal off ers publicly accessible tools of potential use to researchers in neuromuscular disease.",
author = "Matthew Thorley and Apostolos Malatras and Mazza, {Emilia Maria Cristina} and L Zhu and Stephanie Duguez and William Duddy",
year = "2017",
month = "3",
day = "1",
doi = "10.1016/S0960-8966(17)30239-0",
language = "English",
pages = "S8",

}

SysMyo: tailored bioinformatics tools for omics data exploration in muscular dystrophy and other neuromuscular disorders. / Thorley, Matthew; Malatras, Apostolos; Mazza, Emilia Maria Cristina; Zhu, L; Duguez, Stephanie; Duddy, William.

2017. S8.

Research output: Contribution to conferenceAbstract

TY - CONF

T1 - SysMyo: tailored bioinformatics tools for omics data exploration in muscular dystrophy and other neuromuscular disorders

AU - Thorley, Matthew

AU - Malatras, Apostolos

AU - Mazza, Emilia Maria Cristina

AU - Zhu, L

AU - Duguez, Stephanie

AU - Duddy, William

PY - 2017/3/1

Y1 - 2017/3/1

N2 - Background: Most bioinformatics tools and data resources are designed to have wide application, whereas more tailored tools can provide analyses that are adapted to specifi c pathologies or tissue types.Aims: Here we introduce systems biology tools adapted to myology research, currently or soon-to-be accessible through the Sys-Myo web portal (http://sysmyo.rhcloud.com/).Methods: Data are derived from (i) public resources — Gene Expression Omnibus, The Gene Ontology, Uniprot, Mentha, IntAct, GeneMANIA — and (ii) SILAC proteomics combined with immuno pull-down of the Dystrophin protein and its binding partners. Data are collated and analyzed using programmatic tools such as R/Bioconductor and made accessible through a website hosted on the RedHat OpenShift cloud platform. Results: Four tools are introduced. (i) When given a list of genes/proteins, CellWhere returns a network map of gene functional associations overlaid onto a schema of the cell and its subcellular compartments. The tool can be used to screen data for proteins that may be at strongly muscle-relevant cell compartments. (ii) Public transcriptomic data are used to create the Muscle Gene Sets resource, which provides lists of genes that were diff erentially expressed across muscle studies, and can be used for functional enrichment testing. (iii) The Dystrophin Interactome tool combines public functional association data with new SILAC experimental data on the binding partners of the Dystrophin protein, enabling exploration of the functional interactions of this important muscle protein. (iv) MyoMiner will summarize gene co-expression across previous microarray studies of muscle tissues and pathologies, potentially yielding a new empirically-derived defi nition of functional gene clusters in muscle.Conclusions: the Sys-Myo portal off ers publicly accessible tools of potential use to researchers in neuromuscular disease.

AB - Background: Most bioinformatics tools and data resources are designed to have wide application, whereas more tailored tools can provide analyses that are adapted to specifi c pathologies or tissue types.Aims: Here we introduce systems biology tools adapted to myology research, currently or soon-to-be accessible through the Sys-Myo web portal (http://sysmyo.rhcloud.com/).Methods: Data are derived from (i) public resources — Gene Expression Omnibus, The Gene Ontology, Uniprot, Mentha, IntAct, GeneMANIA — and (ii) SILAC proteomics combined with immuno pull-down of the Dystrophin protein and its binding partners. Data are collated and analyzed using programmatic tools such as R/Bioconductor and made accessible through a website hosted on the RedHat OpenShift cloud platform. Results: Four tools are introduced. (i) When given a list of genes/proteins, CellWhere returns a network map of gene functional associations overlaid onto a schema of the cell and its subcellular compartments. The tool can be used to screen data for proteins that may be at strongly muscle-relevant cell compartments. (ii) Public transcriptomic data are used to create the Muscle Gene Sets resource, which provides lists of genes that were diff erentially expressed across muscle studies, and can be used for functional enrichment testing. (iii) The Dystrophin Interactome tool combines public functional association data with new SILAC experimental data on the binding partners of the Dystrophin protein, enabling exploration of the functional interactions of this important muscle protein. (iv) MyoMiner will summarize gene co-expression across previous microarray studies of muscle tissues and pathologies, potentially yielding a new empirically-derived defi nition of functional gene clusters in muscle.Conclusions: the Sys-Myo portal off ers publicly accessible tools of potential use to researchers in neuromuscular disease.

U2 - 10.1016/S0960-8966(17)30239-0

DO - 10.1016/S0960-8966(17)30239-0

M3 - Abstract

SP - S8

ER -