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Public data and open source tools for multi-assay genomic investigation of disease

Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded...

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Autores principales: Kannan, Lavanya, Ramos, Marcel, Re, Angela, El-Hachem, Nehme, Safikhani, Zhaleh, Gendoo, Deena M.A., Davis, Sean, Gomez-Cabrero, David, Castelo, Robert, Hansen, Kasper D., Carey, Vincent J., Morgan, Martin, Culhane, Aedín C., Haibe-Kains, Benjamin, Waldron, Levi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945830/
https://www.ncbi.nlm.nih.gov/pubmed/26463000
http://dx.doi.org/10.1093/bib/bbv080
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author Kannan, Lavanya
Ramos, Marcel
Re, Angela
El-Hachem, Nehme
Safikhani, Zhaleh
Gendoo, Deena M.A.
Davis, Sean
Gomez-Cabrero, David
Castelo, Robert
Hansen, Kasper D.
Carey, Vincent J.
Morgan, Martin
Culhane, Aedín C.
Haibe-Kains, Benjamin
Waldron, Levi
author_facet Kannan, Lavanya
Ramos, Marcel
Re, Angela
El-Hachem, Nehme
Safikhani, Zhaleh
Gendoo, Deena M.A.
Davis, Sean
Gomez-Cabrero, David
Castelo, Robert
Hansen, Kasper D.
Carey, Vincent J.
Morgan, Martin
Culhane, Aedín C.
Haibe-Kains, Benjamin
Waldron, Levi
author_sort Kannan, Lavanya
collection PubMed
description Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.
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spelling pubmed-49458302016-07-19 Public data and open source tools for multi-assay genomic investigation of disease Kannan, Lavanya Ramos, Marcel Re, Angela El-Hachem, Nehme Safikhani, Zhaleh Gendoo, Deena M.A. Davis, Sean Gomez-Cabrero, David Castelo, Robert Hansen, Kasper D. Carey, Vincent J. Morgan, Martin Culhane, Aedín C. Haibe-Kains, Benjamin Waldron, Levi Brief Bioinform Special Issue continued: Computational Systems Biomedicine Papers Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods. Oxford University Press 2016-07 2015-10-10 /pmc/articles/PMC4945830/ /pubmed/26463000 http://dx.doi.org/10.1093/bib/bbv080 Text en © The Author 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Special Issue continued: Computational Systems Biomedicine Papers
Kannan, Lavanya
Ramos, Marcel
Re, Angela
El-Hachem, Nehme
Safikhani, Zhaleh
Gendoo, Deena M.A.
Davis, Sean
Gomez-Cabrero, David
Castelo, Robert
Hansen, Kasper D.
Carey, Vincent J.
Morgan, Martin
Culhane, Aedín C.
Haibe-Kains, Benjamin
Waldron, Levi
Public data and open source tools for multi-assay genomic investigation of disease
title Public data and open source tools for multi-assay genomic investigation of disease
title_full Public data and open source tools for multi-assay genomic investigation of disease
title_fullStr Public data and open source tools for multi-assay genomic investigation of disease
title_full_unstemmed Public data and open source tools for multi-assay genomic investigation of disease
title_short Public data and open source tools for multi-assay genomic investigation of disease
title_sort public data and open source tools for multi-assay genomic investigation of disease
topic Special Issue continued: Computational Systems Biomedicine Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945830/
https://www.ncbi.nlm.nih.gov/pubmed/26463000
http://dx.doi.org/10.1093/bib/bbv080
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