R tools for micro-RNA pathway analysis

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R Tools for microRNA Pathway Analysis
Anwesha Dutta1,2, Pooja R.Mandaviya1,2, Rasanpreet Kaur1,2, Sandeep Mallya1,2, Lars Eijssen1, Susan Coort1, Martijn
P van Iersel1, Jahn Saito1, Prashantha Hebbar2 , Chris T Evelo1.
1. Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands
2. Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India

MicroRNAs are highly conserved and small non-coding RNA molecules. They inhibit
IL-6 signaling Pathway protein expression through translational repression or complete degradation and gene
(Mus musculus) silencing. We integrated validated and predicted miRNAs in biological pathways
available on WikiPathways, using miRNA databases. We linked the validated miRNA
WikiPathways targets to the genes in the pathways, using BridgeDb for identifier mapping. BridgeDb
is a software framework that serves as middleware between relational databases,
files and mapping services. The resulting pathways can be used to investigate miRNAs
expression results from microarray and sequencing technologies. We developed a
Bioconductor package (to be submitted) that uses the existing BridgeDb REST web
services from R. This work is a combined
We verify the miRNA targets in the pathways by co-evaluating miRNA and mRNA effort by the exchange
microarray expression data from a mouse heart failure model. We did this using students of Manipal
arrayanalysis.org, which currently has quality control and normalization modules. We University, India in
added modules for statistical and pathway analysis. Pathway visualization was done collaboration with Dept of
using PathVisio which required connecting R to Java, for which a new XMLRPC Bioinformatics-BiGCaT,
interface was developed. Maastricht University,
Possible Conclusion: we have developed a reusable approach to integrate information about Netherlands.
gene
targets
miRNA in pathways and use these for analyses.

Find miRNAs for target genes miRNA and gene expression microarray analysis

Arrayanalysis.org
Nature Precedings : doi:10.1038/npre.2011.5918.1 : Posted 21 Apr 2011

Mapping services

BridgeDb

Bioinformatics Tools

Identifier Mapping

Analyzed data

PathVisio
Visualization

miRNAs visualized in the pathway

miRNAs added to pathway

Websites used : www.wikipathways.org ; www.bridgedb.org ; www.pathvisio.org ; www.arrayanalysis.org .

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Why Teams call analytics are critical to your entire business

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Exploring the Future Potential of AI-Enabled Smartphone Processors

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Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving

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R tools for micro-RNA pathway analysis

1. R Tools for microRNA Pathway Analysis Anwesha Dutta1,2, Pooja R.Mandaviya1,2, Rasanpreet Kaur1,2, Sandeep Mallya1,2, Lars Eijssen1, Susan Coort1, Martijn P van Iersel1, Jahn Saito1, Prashantha Hebbar2 , Chris T Evelo1. 1. Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands 2. Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India MicroRNAs are highly conserved and small non-coding RNA molecules. They inhibit IL-6 signaling Pathway protein expression through translational repression or complete degradation and gene (Mus musculus) silencing. We integrated validated and predicted miRNAs in biological pathways available on WikiPathways, using miRNA databases. We linked the validated miRNA WikiPathways targets to the genes in the pathways, using BridgeDb for identifier mapping. BridgeDb is a software framework that serves as middleware between relational databases, files and mapping services. The resulting pathways can be used to investigate miRNAs expression results from microarray and sequencing technologies. We developed a Bioconductor package (to be submitted) that uses the existing BridgeDb REST web services from R. This work is a combined We verify the miRNA targets in the pathways by co-evaluating miRNA and mRNA effort by the exchange microarray expression data from a mouse heart failure model. We did this using students of Manipal arrayanalysis.org, which currently has quality control and normalization modules. We University, India in added modules for statistical and pathway analysis. Pathway visualization was done collaboration with Dept of using PathVisio which required connecting R to Java, for which a new XMLRPC Bioinformatics-BiGCaT, interface was developed. Maastricht University, Possible Conclusion: we have developed a reusable approach to integrate information about Netherlands. gene targets miRNA in pathways and use these for analyses. Find miRNAs for target genes miRNA and gene expression microarray analysis Arrayanalysis.org Nature Precedings : doi:10.1038/npre.2011.5918.1 : Posted 21 Apr 2011 Mapping services BridgeDb Bioinformatics Tools Identifier Mapping Analyzed data PathVisio Visualization miRNAs visualized in the pathway miRNAs added to pathway Websites used : www.wikipathways.org ; www.bridgedb.org ; www.pathvisio.org ; www.arrayanalysis.org .