Analysis of spatial distribution of marker expression in cells using boundary distance plots. (English) Zbl 1202.62149

Summary: 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.


62P10 Applications of statistics to biology and medical sciences; meta analysis
62A09 Graphical methods in statistics
92C40 Biochemistry, molecular biology
65C60 Computational problems in statistics (MSC2010)
62H30 Classification and discrimination; cluster analysis (statistical aspects)
92C37 Cell biology


fda (R)
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