Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Santos, Alberto, Tsafou, Kalliopi, Stolte, Christian, Pletscher-Frankild, Sune, O’Donoghue, Seán I., Jensen, Lars Juhl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2015
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
_version_ 1782379956915929088
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
work_keys_str_mv AT santosalberto comprehensivecomparisonoflargescaletissueexpressiondatasets
AT tsafoukalliopi comprehensivecomparisonoflargescaletissueexpressiondatasets
AT stoltechristian comprehensivecomparisonoflargescaletissueexpressiondatasets
AT pletscherfrankildsune comprehensivecomparisonoflargescaletissueexpressiondatasets
AT odonoghueseani comprehensivecomparisonoflargescaletissueexpressiondatasets
AT jensenlarsjuhl comprehensivecomparisonoflargescaletissueexpressiondatasets