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RAIN: RNA–protein Association and Interaction Networks

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challeng...

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Autores principales: Junge, Alexander, Refsgaard, Jan C., Garde, Christian, Pan, Xiaoyong, Santos, Alberto, Alkan, Ferhat, Anthon, Christian, von Mering, Christian, Workman, Christopher T., Jensen, Lars Juhl, Gorodkin, Jan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225963/
https://www.ncbi.nlm.nih.gov/pubmed/28077569
http://dx.doi.org/10.1093/database/baw167
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author Junge, Alexander
Refsgaard, Jan C.
Garde, Christian
Pan, Xiaoyong
Santos, Alberto
Alkan, Ferhat
Anthon, Christian
von Mering, Christian
Workman, Christopher T.
Jensen, Lars Juhl
Gorodkin, Jan
author_facet Junge, Alexander
Refsgaard, Jan C.
Garde, Christian
Pan, Xiaoyong
Santos, Alberto
Alkan, Ferhat
Anthon, Christian
von Mering, Christian
Workman, Christopher T.
Jensen, Lars Juhl
Gorodkin, Jan
author_sort Junge, Alexander
collection PubMed
description Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain
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spelling pubmed-52259632017-01-18 RAIN: RNA–protein Association and Interaction Networks Junge, Alexander Refsgaard, Jan C. Garde, Christian Pan, Xiaoyong Santos, Alberto Alkan, Ferhat Anthon, Christian von Mering, Christian Workman, Christopher T. Jensen, Lars Juhl Gorodkin, Jan Database (Oxford) Original Article Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain Oxford University Press 2017-01-10 /pmc/articles/PMC5225963/ /pubmed/28077569 http://dx.doi.org/10.1093/database/baw167 Text en © The Author(s) 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Original Article
Junge, Alexander
Refsgaard, Jan C.
Garde, Christian
Pan, Xiaoyong
Santos, Alberto
Alkan, Ferhat
Anthon, Christian
von Mering, Christian
Workman, Christopher T.
Jensen, Lars Juhl
Gorodkin, Jan
RAIN: RNA–protein Association and Interaction Networks
title RAIN: RNA–protein Association and Interaction Networks
title_full RAIN: RNA–protein Association and Interaction Networks
title_fullStr RAIN: RNA–protein Association and Interaction Networks
title_full_unstemmed RAIN: RNA–protein Association and Interaction Networks
title_short RAIN: RNA–protein Association and Interaction Networks
title_sort rain: rna–protein association and interaction networks
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225963/
https://www.ncbi.nlm.nih.gov/pubmed/28077569
http://dx.doi.org/10.1093/database/baw167
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