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Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas

The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. These are currently annotated by visual inspection. In this paper, we describe automated approaches to analyze the images and their use to improve annotation. We began by training clas...

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Detalles Bibliográficos
Autores principales: Li, Jieyue, Newberg, Justin Y., Uhlén, Mathias, Lundberg, Emma, Murphy, Robert F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511558/
https://www.ncbi.nlm.nih.gov/pubmed/23226299
http://dx.doi.org/10.1371/journal.pone.0050514
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author Li, Jieyue
Newberg, Justin Y.
Uhlén, Mathias
Lundberg, Emma
Murphy, Robert F.
author_facet Li, Jieyue
Newberg, Justin Y.
Uhlén, Mathias
Lundberg, Emma
Murphy, Robert F.
author_sort Li, Jieyue
collection PubMed
description The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. These are currently annotated by visual inspection. In this paper, we describe automated approaches to analyze the images and their use to improve annotation. We began by training classifiers to recognize the annotated patterns. By ranking proteins according to the confidence of the classifier, we generated a list of proteins that were strong candidates for reexamination. In parallel, we applied hierarchical clustering to group proteins and identified proteins whose annotations were inconsistent with the remainder of the proteins in their cluster. These proteins were reexamined by the original annotators, and a significant fraction had their annotations changed. The results demonstrate that automated approaches can provide an important complement to visual annotation.
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spelling pubmed-35115582012-12-05 Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas Li, Jieyue Newberg, Justin Y. Uhlén, Mathias Lundberg, Emma Murphy, Robert F. PLoS One Research Article The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. These are currently annotated by visual inspection. In this paper, we describe automated approaches to analyze the images and their use to improve annotation. We began by training classifiers to recognize the annotated patterns. By ranking proteins according to the confidence of the classifier, we generated a list of proteins that were strong candidates for reexamination. In parallel, we applied hierarchical clustering to group proteins and identified proteins whose annotations were inconsistent with the remainder of the proteins in their cluster. These proteins were reexamined by the original annotators, and a significant fraction had their annotations changed. The results demonstrate that automated approaches can provide an important complement to visual annotation. Public Library of Science 2012-11-30 /pmc/articles/PMC3511558/ /pubmed/23226299 http://dx.doi.org/10.1371/journal.pone.0050514 Text en © 2012 Li 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Li, Jieyue
Newberg, Justin Y.
Uhlén, Mathias
Lundberg, Emma
Murphy, Robert F.
Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas
title Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas
title_full Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas
title_fullStr Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas
title_full_unstemmed Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas
title_short Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas
title_sort automated analysis and reannotation of subcellular locations in confocal images from the human protein atlas
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511558/
https://www.ncbi.nlm.nih.gov/pubmed/23226299
http://dx.doi.org/10.1371/journal.pone.0050514
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