Cargando…
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...
Autores principales: | , , , , , , , , , , |
---|---|
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 |
_version_ | 1782493604327981056 |
---|---|
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 |
format | Online Article Text |
id | pubmed-5225963 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT jungealexander rainrnaproteinassociationandinteractionnetworks AT refsgaardjanc rainrnaproteinassociationandinteractionnetworks AT gardechristian rainrnaproteinassociationandinteractionnetworks AT panxiaoyong rainrnaproteinassociationandinteractionnetworks AT santosalberto rainrnaproteinassociationandinteractionnetworks AT alkanferhat rainrnaproteinassociationandinteractionnetworks AT anthonchristian rainrnaproteinassociationandinteractionnetworks AT vonmeringchristian rainrnaproteinassociationandinteractionnetworks AT workmanchristophert rainrnaproteinassociationandinteractionnetworks AT jensenlarsjuhl rainrnaproteinassociationandinteractionnetworks AT gorodkinjan rainrnaproteinassociationandinteractionnetworks |