Analysis of spatial distribution of marker expression in cells using boundary distance plots

DOI10.1214/10-AOAS340MaRDI QIDQ614152zbMATH OpenFDO

Authors Kingshuk Roy Choudhury, Limian Zheng, John J. Mackrill

Publication date 27 December 2010

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1011.3309

zbMATH Keywords

functional data analysissmoothingcurve registrationEuclidean distance transformimage texture

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Graphical methods in statistics (62A09) Cell biology (92C37)

Abstract: Boundary distance (BD) plotting is a technique for making orientation invariant comparisons of the spatial distribution of biochemical markers within and across cells/nuclei. Marker expression is aggregated over points with the same distance from the boundary. We present a suite of tools for improved data analysis and statistical inference using BD plotting. BD is computed using the Euclidean distance transform after presmoothing and oversampling of nuclear boundaries. Marker distribution profiles are averaged using smoothing with linearly decreasing bandwidth. Average expression curves are scaled and registered by x-axis dilation to compensate for uneven lighting and errors in nuclear boundary marking. Penalized discriminant analysis is used to characterize the quality of separation between average marker distributions. An adaptive piecewise linear model is used to compare expression gradients in intra, peri and extra nuclear zones. The techniques are illustrated by the following: (a) a two sample problem involving a pair of voltage gated calcium channels (Cav1.2 and AB70) marked in different cells; (b) a paired sample problem of calcium channels (Y1F4 and RyR1) marked in the same cell.

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Cites work

• scientific article; zbMATH DE number 3980241 (Why is no real title available?)
• scientific article; zbMATH DE number 1964693 (Why is no real title available?)
• Applied functional data analysis. Methods and case studies
• Optimal convergence properties of variable knot, kernel, and orthogonal series methods for density estimation
• Spline smoothing: The equivalent variable kernel method
• The elements of statistical learning. Data mining, inference, and prediction

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• fda (R)

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