GCPReg package for registration of the segmentation gene expression data in Drosophila

Abstract

In modern functional genomics registration techniques areused to construct reference gene expression patterns and createa spatiotemporal atlas of the expression of all the genes in anetwork. In this paper we present a software package calledGCPReg, which can be used to register the expression patterns ofsegmentation genes in the early Drosophila embryo. The key task,which this package performs, is the extraction of spatially localizedcharacteristic features of expression patterns. To facilitatethis task, we have developed an easy-to-use interactive graphicalinterface. We describe GCPReg usage and demonstrate how thispackage can be applied to register gene expression patterns inwild type and mutants. GCPReg has been designed to operate ona UNIX platform and is freely available via the Internet at http://urchin.spbcas.ru/downloads/GCPReg/GCPReg.htm.

Figure 1

GCPReg interface.

Figure 2

GUI for extraction of the GCP template. The template is constructed for eve expression pattern in embryos mutant for Kr belonging to late cycle 14A (time class 6 according to our classification, see Materials and methods). The Dataset panel (left) shows the folders containing the dataset. Any number of files can be selected and moved to the Selected panel by pressing the Add button. The upper panel on the right (Individual) presents the graphs of selected patterns; while in the lower panel (Averaged) the average of these patterns is plotted. The pop-up menu shows cursor coordinates and the list of feasible GCPs.

Figure 3

Feature extraction and registration. (A) The FRDWT decomposition of eve pattern in the wild-type embryo belonging to late cycle 14A (time class 6). The pattern is decomposed into two sequences, low pass and high pass, and GCPs are extracted as zeros of the high pass and marked on the pattern by arrows. (B) Spline approximation of eve pattern in a Kr⁻ mutant embryo from the time class 5. GCPs are extracted as coordinates of the spline extrema (marked by arrows). (C) GUI for interactive correction of the automatically found GCPs. In this pattern the fifth GCP (third maximum) is misplaced and needs to be corrected (the corresponding GCP template is shown in Fig. 2). (D) Visualization of registration results: the registered pattern is superimposed on the reference pattern. (E and F) Screenshots of registration results: three eve patterns in Kr⁻ embryos before (E) and after (F) registration. The expression pattern presented in (C and D) is the same as in (B).

Figure 4

GCPReg usage examples: Screenshots of registration results. (A) Automated registration: five expression patterns of the eve gene in embryos belonging to late cycle 14A (time class 6) before (A1) and after (A2) registration. (B) Induced registration: Three Kr expression patterns acquired in the same embryos as the eve patterns presented in (A1 and A2) and registered using these patterns. (C) Interactive registration: The GCP extraction from slp expression pattern in an embryo belonging to late cycle 14A. Maxima of stripes from 1 to 7 are only used as GCPs. (D) Results of the interactive registration of four late slp expression patterns in wild-type embryos from time class 8. Expression domains are enumerated from 0 to 7.