gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.

Farancesco Napolitano; Diego Carrella; Xin Gao; Diego di Bernardo

doi:10.1093/bioinformatics/btz803

gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.

Farancesco Napolitano, Diego Carrella, Xin Gao, Diego di Bernardo

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Abstract

SUMMARY:Pathway-based expression profiles allow for high-level interpretation of transcriptomic data and systematic comparison of dysregulated cellular programs. We have previously demonstrated the efficacy of pathway-based approaches with two different applications: the Drug Set Enrichment Analysis and the Gene2drug analysis. Here we present a software tool that allows to easily convert gene-based profiles to pathway-based profiles and analyze them within the popular R framework. We also provide pre-computed profiles derived from the original Connectivity Map and its next generation release, i.e. the LINCS database. AVAILABILITY AND IMPLEMENTATION:the tool is implemented as the R/Bioconductor package gep2pep and can be freely downloaded from https://bioconductor.org/packages/gep2pep. SUPPLEMENTARY INFORMATION:Supplementary data are available at http://dsea.tigem.it/lincs.

Original language	English (US)
Journal	Bioinformatics (Oxford, England)
DOIs	https://doi.org/10.1093/bioinformatics/btz803
State	Published - Oct 25 2019

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10.1093/bioinformatics/btz803

https://repository.kaust.edu.sa/bitstream/10754/660056/1/btz803.pdf

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@article{cd8c22cfb5a349f8af05c4fe70743f13,

title = "gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.",

abstract = "SUMMARY:Pathway-based expression profiles allow for high-level interpretation of transcriptomic data and systematic comparison of dysregulated cellular programs. We have previously demonstrated the efficacy of pathway-based approaches with two different applications: the Drug Set Enrichment Analysis and the Gene2drug analysis. Here we present a software tool that allows to easily convert gene-based profiles to pathway-based profiles and analyze them within the popular R framework. We also provide pre-computed profiles derived from the original Connectivity Map and its next generation release, i.e. the LINCS database. AVAILABILITY AND IMPLEMENTATION:the tool is implemented as the R/Bioconductor package gep2pep and can be freely downloaded from https://bioconductor.org/packages/gep2pep. SUPPLEMENTARY INFORMATION:Supplementary data are available at http://dsea.tigem.it/lincs.",

author = "Farancesco Napolitano and Diego Carrella and Xin Gao and {di Bernardo}, Diego",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: Funding: This work has been supported by Fondazione Telethon and Fondazione Veronesi.",

year = "2019",

month = oct,

day = "25",

doi = "10.1093/bioinformatics/btz803",

language = "English (US)",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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TY - JOUR

T1 - gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.

AU - Napolitano, Farancesco

AU - Carrella, Diego

AU - Gao, Xin

AU - di Bernardo, Diego

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: Funding: This work has been supported by Fondazione Telethon and Fondazione Veronesi.

PY - 2019/10/25

Y1 - 2019/10/25

N2 - SUMMARY:Pathway-based expression profiles allow for high-level interpretation of transcriptomic data and systematic comparison of dysregulated cellular programs. We have previously demonstrated the efficacy of pathway-based approaches with two different applications: the Drug Set Enrichment Analysis and the Gene2drug analysis. Here we present a software tool that allows to easily convert gene-based profiles to pathway-based profiles and analyze them within the popular R framework. We also provide pre-computed profiles derived from the original Connectivity Map and its next generation release, i.e. the LINCS database. AVAILABILITY AND IMPLEMENTATION:the tool is implemented as the R/Bioconductor package gep2pep and can be freely downloaded from https://bioconductor.org/packages/gep2pep. SUPPLEMENTARY INFORMATION:Supplementary data are available at http://dsea.tigem.it/lincs.

AB - SUMMARY:Pathway-based expression profiles allow for high-level interpretation of transcriptomic data and systematic comparison of dysregulated cellular programs. We have previously demonstrated the efficacy of pathway-based approaches with two different applications: the Drug Set Enrichment Analysis and the Gene2drug analysis. Here we present a software tool that allows to easily convert gene-based profiles to pathway-based profiles and analyze them within the popular R framework. We also provide pre-computed profiles derived from the original Connectivity Map and its next generation release, i.e. the LINCS database. AVAILABILITY AND IMPLEMENTATION:the tool is implemented as the R/Bioconductor package gep2pep and can be freely downloaded from https://bioconductor.org/packages/gep2pep. SUPPLEMENTARY INFORMATION:Supplementary data are available at http://dsea.tigem.it/lincs.

UR - http://hdl.handle.net/10754/660056

UR - https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz803/5606711

U2 - 10.1093/bioinformatics/btz803

DO - 10.1093/bioinformatics/btz803

M3 - Article

C2 - 31647521

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

ER -

gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.

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