A framework for the automated analysis of subcellular patterns in human protein atlas images.

Journal of Proteome Research
Justin Newberg, Robert F Murphy

Abstract

The systematic study of subcellular location patterns is required to fully characterize the human proteome, as subcellular location provides critical context necessary for understanding a protein's function. The analysis of tens of thousands of expressed proteins for the many cell types and cellular conditions under which they may be found creates a need for automated subcellular pattern analysis. We therefore describe the application of automated methods, previously developed and validated by our laboratory on fluorescence micrographs of cultured cell lines, to analyze subcellular patterns in tissue images from the Human Protein Atlas. The Atlas currently contains images of over 3000 protein patterns in various human tissues obtained using immunohistochemistry. We chose a 16 protein subset from the Atlas that reflects the major classes of subcellular location. We then separated DNA and protein staining in the images, extracted various features from each image, and trained a support vector machine classifier to recognize the protein patterns. Our results show that our system can distinguish the patterns with 83% accuracy in 45 different tissues, and when only the most confident classifications are considered, this rises to 97%....Continue Reading

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Citations

Mar 18, 2010·Nature Methods·Thomas WalterJean-Karim Hériché
Dec 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Michael D SlackSteven J Altschuler
Jul 8, 2008·Bioinformatics·Hanchuan Peng
Jul 16, 2010·Bioinformatics·Timo ErkkiläHarri Lähdesmäki
Mar 24, 2009·BMC Bioinformatics·Nicholas A HamiltonRohan D Teasdale
May 3, 2011·BMC Bioinformatics·Bailing Zhang, Tuan D Pham
Jun 15, 2013·Journal of Pathology Informatics·Issac Niwas SwamidossRobin Strand
Dec 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Aparna KumarRobert F Murphy
Jul 11, 2012·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Taráz E BuckRobert F Murphy
Jan 1, 2009·IEEE Reviews in Biomedical Engineering·Metin N GurcanB Yener
Jan 17, 2013·IEEE Transactions on Medical Imaging·Milan GavrilovicIngrid B Carlbom
Nov 28, 2012·Biochemical Society Transactions·Vasanth R SinganJeremy C Simpson
Dec 3, 2014·Fertility and Sterility·Carolina J JorgezDolores J Lamb
May 22, 2010·Journal of Biomolecular Screening·Aabid ShariffRobert F Murphy
Dec 2, 2015·IEEE Journal of Biomedical and Health Informatics·Xingyu Li, Konstantinos N Plataniotis
Mar 10, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Wei ShaoDaoqiang Zhang
Mar 15, 2018·Journal of Medical Signals and Sensors·Keyvan JabbariMohammad B Tavakoli
Aug 24, 2021·Molecular & Cellular Proteomics : MCP·Biraja GhoshalCecilia Lindskog

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