A review of connectivity map and computational approaches in pharmacogenomics

Abstract Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing...

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Published inBriefings in bioinformatics Vol. 19; no. 3; pp. 506 - 523
Main Authors Musa, Aliyu, Ghoraie, Laleh Soltan, Zhang, Shu-Dong, Glazko, Galina, Yli-Harja, Olli, Dehmer, Matthias, Haibe-Kains, Benjamin, Emmert-Streib, Frank
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.05.2018
Oxford Publishing Limited (England)
Subjects
Cellular communication
Computational Biology - methods
Computer applications
Computer networks
Databases, Factual
drug design
Drug development
Gene Expression Profiling - methods
Gene Regulatory Networks
Humans
Perturbation
Pharmacogenetics
Pharmacogenomics
Pharmacology
Small Molecule Libraries - pharmacology
Transcriptome
transcriptomics
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Abstract Abstract Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
AbstractList Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
Abstract Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
Author Yli-Harja, Olli
Emmert-Streib, Frank
Glazko, Galina
Haibe-Kains, Benjamin
Ghoraie, Laleh Soltan
Zhang, Shu-Dong
Dehmer, Matthias
Musa, Aliyu
AuthorAffiliation 5 Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
7 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
9 Ontario Institute of Cancer Research, Toronto, ON, Canada
6 Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, Hall in Tyrol, Austria
4 University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York, USA
1 Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
3 Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, Northern Ireland, UK
2 Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
8 Department o
AuthorAffiliation_xml – name: 4 University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York, USA
– name: 8 Department of Computer Science, University of Toronto, Toronto, ON, Canada
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– name: 6 Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, Hall in Tyrol, Austria
– name: 7 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
– name: 1 Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
– name: 3 Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, Northern Ireland, UK
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  email: frank.emmert-streib@tut.fi
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  givenname: Laleh Soltan
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  organization: Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, Northern Ireland, UK
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  surname: Dehmer
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  surname: Emmert-Streib
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  email: frank.emmert-streib@tut.fi
  organization: Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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PublicationDate_xml – month: 05
  year: 2018
  text: 2018-05-01
  day: 01
PublicationDecade 2010
PublicationPlace England
PublicationPlace_xml – name: England
– name: Oxford
PublicationTitle Briefings in bioinformatics
PublicationTitleAlternate Brief Bioinform
PublicationYear 2018
Publisher Oxford University Press
Oxford Publishing Limited (England)
Publisher_xml – name: Oxford University Press
– name: Oxford Publishing Limited (England)
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Snippet Abstract Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide...
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous...
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StartPage 506
SubjectTerms Cellular communication
Computational Biology - methods
Computer applications
Computer networks
Databases, Factual
drug design
Drug development
Gene Expression Profiling - methods
Gene Regulatory Networks
Humans
Perturbation
Pharmacogenetics
Pharmacogenomics
Pharmacology
Small Molecule Libraries - pharmacology
Transcriptome
transcriptomics
Title A review of connectivity map and computational approaches in pharmacogenomics
URI https://www.ncbi.nlm.nih.gov/pubmed/28069634
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https://pubmed.ncbi.nlm.nih.gov/PMC5952941
Volume 19
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