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Footprint-based functional analysis of multiomic data
Omic technologies allow us to generate extensive data, including transcriptomic, proteomic, phosphoproteomic and metabolomic. These data can be used to study signal transduction, gene regulation and metabolism. In this review, we summarise resources and methods to analysis these types of data. We fo...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier Ltd
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357600/ https://www.ncbi.nlm.nih.gov/pubmed/32685770 http://dx.doi.org/10.1016/j.coisb.2019.04.002 |
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author | Dugourd, Aurelien Saez-Rodriguez, Julio |
author_facet | Dugourd, Aurelien Saez-Rodriguez, Julio |
author_sort | Dugourd, Aurelien |
collection | PubMed |
description | Omic technologies allow us to generate extensive data, including transcriptomic, proteomic, phosphoproteomic and metabolomic. These data can be used to study signal transduction, gene regulation and metabolism. In this review, we summarise resources and methods to analysis these types of data. We focus on methods developed to recover functional insights using footprints. Footprints are signatures defined by the effect of molecules or processes of interest. They integrate information from multiple measurements whose abundances are under the influence of a common regulator. For example, transcripts controlled by a transcription factor or peptides phosphorylated by a kinase. Footprints can also be generalised across multiple types of omic data. Thus, we also present methods to integrate multiple types of omic data and features (such as the ones derived from footprints) together. We highlight some examples of studies that leverage such approaches to discover new biological mechanisms. |
format | Online Article Text |
id | pubmed-7357600 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Elsevier Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-73576002020-07-17 Footprint-based functional analysis of multiomic data Dugourd, Aurelien Saez-Rodriguez, Julio Curr Opin Syst Biol Article Omic technologies allow us to generate extensive data, including transcriptomic, proteomic, phosphoproteomic and metabolomic. These data can be used to study signal transduction, gene regulation and metabolism. In this review, we summarise resources and methods to analysis these types of data. We focus on methods developed to recover functional insights using footprints. Footprints are signatures defined by the effect of molecules or processes of interest. They integrate information from multiple measurements whose abundances are under the influence of a common regulator. For example, transcripts controlled by a transcription factor or peptides phosphorylated by a kinase. Footprints can also be generalised across multiple types of omic data. Thus, we also present methods to integrate multiple types of omic data and features (such as the ones derived from footprints) together. We highlight some examples of studies that leverage such approaches to discover new biological mechanisms. Elsevier Ltd 2019-06 /pmc/articles/PMC7357600/ /pubmed/32685770 http://dx.doi.org/10.1016/j.coisb.2019.04.002 Text en © 2019 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Dugourd, Aurelien Saez-Rodriguez, Julio Footprint-based functional analysis of multiomic data |
title | Footprint-based functional analysis of multiomic data |
title_full | Footprint-based functional analysis of multiomic data |
title_fullStr | Footprint-based functional analysis of multiomic data |
title_full_unstemmed | Footprint-based functional analysis of multiomic data |
title_short | Footprint-based functional analysis of multiomic data |
title_sort | footprint-based functional analysis of multiomic data |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357600/ https://www.ncbi.nlm.nih.gov/pubmed/32685770 http://dx.doi.org/10.1016/j.coisb.2019.04.002 |
work_keys_str_mv | AT dugourdaurelien footprintbasedfunctionalanalysisofmultiomicdata AT saezrodriguezjulio footprintbasedfunctionalanalysisofmultiomicdata |