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Comprehensive comparison of large-scale tissue expression datasets
For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a compr...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493645/ https://www.ncbi.nlm.nih.gov/pubmed/26157623 http://dx.doi.org/10.7717/peerj.1054 |
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author | Santos, Alberto Tsafou, Kalliopi Stolte, Christian Pletscher-Frankild, Sune O’Donoghue, Seán I. Jensen, Lars Juhl |
author_facet | Santos, Alberto Tsafou, Kalliopi Stolte, Christian Pletscher-Frankild, Sune O’Donoghue, Seán I. Jensen, Lars Juhl |
author_sort | Santos, Alberto |
collection | PubMed |
description | For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression. By developing comparable confidence scores for all types of evidence, we show that it is possible to improve both quality and coverage by combining the datasets. To facilitate use and visualization of our work, we have developed the TISSUES resource (http://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface. |
format | Online Article Text |
id | pubmed-4493645 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-44936452015-07-08 Comprehensive comparison of large-scale tissue expression datasets Santos, Alberto Tsafou, Kalliopi Stolte, Christian Pletscher-Frankild, Sune O’Donoghue, Seán I. Jensen, Lars Juhl PeerJ Computational Biology For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression. By developing comparable confidence scores for all types of evidence, we show that it is possible to improve both quality and coverage by combining the datasets. To facilitate use and visualization of our work, we have developed the TISSUES resource (http://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface. PeerJ Inc. 2015-06-30 /pmc/articles/PMC4493645/ /pubmed/26157623 http://dx.doi.org/10.7717/peerj.1054 Text en © 2015 Santos et al. 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 use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Computational Biology Santos, Alberto Tsafou, Kalliopi Stolte, Christian Pletscher-Frankild, Sune O’Donoghue, Seán I. Jensen, Lars Juhl Comprehensive comparison of large-scale tissue expression datasets |
title | Comprehensive comparison of large-scale tissue expression datasets |
title_full | Comprehensive comparison of large-scale tissue expression datasets |
title_fullStr | Comprehensive comparison of large-scale tissue expression datasets |
title_full_unstemmed | Comprehensive comparison of large-scale tissue expression datasets |
title_short | Comprehensive comparison of large-scale tissue expression datasets |
title_sort | comprehensive comparison of large-scale tissue expression datasets |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493645/ https://www.ncbi.nlm.nih.gov/pubmed/26157623 http://dx.doi.org/10.7717/peerj.1054 |
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