Abstract
Location proteomics is the systematic study of subcellular locations of proteins. It seeks to provide a thorough understanding of location patterns and integrate such knowledge into systems biology studies. Progress in this field depends on the quantitative and automated analysis of images of location patterns. This chapter introduces various approaches to such analysis and summarizes successes in using them to investigate different image types and different cell types.
These approaches can be divided into two categories, feature-based analysis, and pattern modeling. In feature-based analysis, each image is converted into a feature vector and all further analysis is carried out on the features. This has enabled the automated comparison, classification, and clustering of location patterns on a large scale. An important conclusion from this work has been that, at least for certain problems, computerized analysis can perform better than visual examination. To take a further step, object-based models have been built to describe location patterns in a compact and portable form. This facilitates more complicated analysis, such as the decomposition of patterns that are themselves mixtures of more basic patterns. Moreover, generative models can be learned from collections of images so that new examples of location patterns can be synthesized from them. This provides a way to integrate location information into systems biology, by combining generative models of many proteins and using the synthesized images as initial conditions for cell behavior simulations.
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References
Karim R, Tse G, Putti T, et al. The significance of the Wnt pathway in the pathology of human cancers. Pathology 2004;36(2):120–128.
White MA, Anderson RGW. Signaling networks in living cells. Annu Rev Pharmacol Toxicol 2005;45:587–603.
Harris MA, Clark J, Ireland A, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004;32:D258–D61.
Horton P, Nakai K. Better Prediction of Protein Cellular Localization Sites with the k Nearest Neighbors Classifier. Intell Sys Mol Biol 1997;5:147–152.
Nakai K. Protein sorting signals and prediction of subcellular localization. Adv Protein Chem 2000;54:277–344.
Hua S, Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics 2001;17(8):721–728.
Lu Z, Szafron D, Greiner R, et al. Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics 2004;20(4):547–556.
Chou K-C, Elrod DW. Protein subcellular location prediction. Protein Eng 1999;12(2):107–118.
Boland MV, Murphy RF. A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics 2001;17(12):1213–1223.
Chen X, Murphy RF. Objective clustering of proteins based on subcellular location patterns. J Biomed Biotechnol 2005;2005(2):87–95.
Eisenberg D, Marcotte E, McLachlan AD, et al. Bioformatic challenges for the next decade(s). Phil Trans R Soc B 2006;Published online.
Dreger M. Proteome analysis at the level of subcellular structures. Eur J Biochem 2003;270:589–599.
Brunet STP, Gagnon E, Kearney P, et al. Organelle proteomics: looking at less to see more. Trends Cell Biol 2003;13(12):629–638.
Yates JR 3rd, Gilchrist A, Howell KE, et al. Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol 2005;6(9):702–714.
Huh W-K, Falvo JV, Gerke LC, et al. Global analysis of protein localization in budding yeast. Nature 2003;425(6959):686–691.
Simpson JC, Wellenreuther R, Poustka A, et al. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep 2000;1(3):287–292.
Jarvik JW, Fisher GW, Shi C, et al. In vivo functional proteomics: Mammalian genome annotation using CD-tagging. Biotechniques 2002;33(4):852–867.
Chen X, Velliste M, Weinstein S, et al. Location proteomics—building subcellular location trees from high resolution 3D fluorescence microscope images of randomly-tagged proteins. Proc SPIE 2003;4962:298–306.
Chen X, Murphy RF. Location proteomics: determining the optimal groupings of proteins according to their subcellular location patterns as determined from fluorescence microscope images. In: Proceedings of 2004 Asilomar Workshop on Signals, Systems and Computers. 2004:50–54.
Uhlén M, Björling E, Agaton C, et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Amer Soc Biochem Mol Biol 2005;4:1920–1932.
Huang K, Murphy RF. From quantitative microscopy to automated image understanding. J Biomed Optics 2004;9(5):893–912.
Huang K, Murphy RF. Data mining methods for a systematics of protein subcellular location. In: Wang JTL, Zaki MJ, Toivonen HTT, Shasha D, eds. Data Mining in Bioinformatics. London: Springer-Verlag; 2004:143–187.
Jones TR, Carpenter AE, Golland P. Voronoi-based segmentation of cells on image manifolds. In: Proceedings of ICCV Workshop on Computer Vision for Biomedical Image Applications. 2005:535–543.
De Solorzano CO, Malladi R, Lelievre SA, et al. Segmentation of nuclei and cells using membrane related protein markers. J Microsci 2001;201 (Pt 3):404–415.
Lotufo R, Falcao A. The ordered queue and the optimality of the watershed approaches. In: Goutsias J, Vincent L, Bloomberg DS, eds. Mathematical Morphology and its Application to Image and Signal Processing: Kluwer Academic Publishers; 2000.
Velliste M, Murphy RF. Automated determination of protein subcellular locations from 3D fluorescence microscope images. In: Proceedings of 2002 IEEE International Symposium on Biomedical Imaging (ISBI-2002). 2002:867–870.
Coulot L, Kirschner H, Chebira A, et al. Topology preserving STACS segmentation of protein subcellular location images. In: Proceedings of 2006 IEEE International Symposium on Biomedical Imaging (ISBI-2006). 2006:566–569.
Huang K, Velliste M, Murphy RF. Feature reduction for improved recognition of subcellular location patterns in fluorescence microscope images. Proc SPIE 2003;4962:307–318.
Jennrich RI. Stepwise discriminant analysis. In: Enslein K, Ralston A, Wilf HS, eds. Statistical Methods for Digital Computers. New York: John Wiley & Sons; 1977:77–95.
Boland MV, Markey MK, Murphy RF. Classification of protein localization patterns obtained via fluorescence light microscopy. In: Proceedings of 19th Annual International Conference of the IEEE Engineering in Medicine and Biology Society; 1997:594–597.
Boland MV, Markey MK, Murphy RF. Automated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images. Cytometry 1998;33(3):366–75.
Huang K, Murphy RF. Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. BMC Bioinformatics 2004;5:78.
Murphy RF, Velliste M, Porreca G. Robust numerical features for description and classification of subcellular location patterns in fluorescence microscope images. J VLSI Sig Proc 2003;35(3):311–321.
Chen X, Murphy RF. Robust Classification of Subcellular Location Patterns in High Resolution 3D Fluorescence Microscopy Images. In: Proceedings of 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2004:1632–1635.
Conrad C, Erfle H, Warnat P, et al. Automatic identification of subcellular phenotypes on human cell arrays. Genome Res 2004;14:1130–1136.
Zhao T, Velliste M, Boland MV, et al. Object Type Recognition for Automated Analysis of Protein Subcellular Location. IEEE Trans on Image Processing 2005;14(9):1351–1359.
Hu Y, Carmona J, Murphy RF. Application of temporal texture features to automated analysis of protein subcellular locations in time series fluorescence microscope images. In: Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging (ISBI 2006); 2006; 2006. pp. 1028–1031.
Roques EJS, Murphy RF. Objective evaluation of differences in protein subcellular distribution. Traffic 2002;3(1):61–65.
Chen X, Velliste M, Murphy RF. Automated interpretation of subcellular patterns in fluorescence microscope images for location proteomics. Cytometry 2006;69A:631–640.
Murphy RF. Automated interpretation of subcellular location patterns. In: 2004 IEEE International Symposium on Biomedical Imaging (ISBI-2004). 2004. 53–56.
Murphy RF. Cytomics and location proteomics: automated interpretation of subcellular patterns in fluorescence microscope images. Cytometry 2005;67A:1–3.
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Zhao, T., Chen, SC., Murphy, R.F. (2007). Location Proteomics. In: Choi, S. (eds) Introduction to Systems Biology. Humana Press. https://doi.org/10.1007/978-1-59745-531-2_11
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DOI: https://doi.org/10.1007/978-1-59745-531-2_11
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