Abstract
To understand transcriptional regulation during development a detailed analysis of gene expression is needed. In-situ hybridization experiments measure the spatial distribution of mRNA-molecules and thus complement DNA-microarray experiments. This is of very high biological relevance, as co-location is a necessary condition for possible molecular interactions.
We use publicly available in-situ data from embryonal development of Drosophila and derive a co-location index for pairs of genes. Our image processing pipeline for in-situ images provides a simpler alternative for the image processing part at comparable performance compared to published prior work. We formulate a mixture model which can use the pair-wise co-location indices as constraints in a mixture estimation on gene expression time-courses.
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References
BAR-JOSEPH, Z. (2004): Analyzing Time Series Gene Expression Data. Bioinformatics, 20,16, 2493–2503
GONZALES, R. and WINTZ, P. (1991): Digital Image Processing. Addison-Wesley.
KUMAR, S., JAYARAMAN, K., PANCHANATHAN, S., GURUNATHAN, R., MARTI-SUBIRANA, A. and NEWFIELD, S. (2002): BEST — A Novel Computational Approach for Comparing Gene Expression Patterns from Early Stages of Drosophila Melanogaster Development. Genetics, 169, 2037–2047.
LANGE, T., LAW, M.H., JAIN, A.K. and BUHMANN, J.M. (2005): Learning with Constrained and Unlabeled Data. IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1, 731–738.
LU, Z. and LEEN, T. (2005): Semi-supervised Learning with Penalized Probabilistic Clustering. NIPS 17, 849–856.
MCLACHLAN, G. and PEEL, D. (2000): Finite Mixture Models. Wiley, New-York.
NEUMANN, S., POSCH, S. and SAGERER, G. (1999): Towards Evaluation of Docking Hypothesis Using Elastic Matching. Proceedings of the GCB, 220.
OPITZ, L. (2005): Analyse von Bildern der mRNA-in Situ-Hybridisierung. Master thesis, Institut für Informatik, Universität Halle-Wittenberg.
PENG, H. and MYERS, E.W. (2004): Comparing in situ mRNA Expression Patterns of Drosophila Embryos. RECOMB’04, 157–166.
SCHLIEP, A., COSTA, I.G., STEINHOFF, C. and SCHÖNHUTH (2005): Analyzing Gene Expression Time-courses. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2,3, 179–193.
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Opitz, L., Schliep, A., Posch, S. (2007). Joint Analysis of In-situ Hybridization and Gene Expression Data. In: Decker, R., Lenz, H.J. (eds) Advances in Data Analysis. Studies in Classification, Data Analysis, and Knowledge Organization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70981-7_66
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DOI: https://doi.org/10.1007/978-3-540-70981-7_66
Publisher Name: Springer, Berlin, Heidelberg
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