The homeobox genes of Caenorhabditis elegans and insights into their spatio-temporal expression dynamics during embryogenesis

Jürgen Hench^*, Johan Henriksson^*, Akram M. Abou-Zied, Martin Lüppert, Johan Dethlefsen, Krishanu Mukherjee, Yong-Guang Tong, Lois Tang, Umesh Gangishetti, David Baillie, and Thomas R. Bürglin^#

* equal contribution
# corresponding author: thomas.buerglin AT unibas.ch

See also Endrov, the software we used to analyze this data

Thumbnail Movies of expression patterns

Movies marked "quantified" are the ones from which expression profiles have been extracted. Other movies are included because they contain information of qualitative value.
The movies are in the free Theora format and can be played out-of-the-box with modern webbrowsers such as Firefox, Chrome and Opera. Internet Explorer and Safari do not yet support it. The movies can also be downloaded and played using VLC.

OSX: Install Perian to get the codecs (Note: Still works on OSX 10.10, despite no longer being supported
Windows: Install FFMPEG for DirectShow to get the codecs
Linux: You probably have the codecs already. Seeking in Firefox is slow - open the movies in VLC instead.

Summary figures of expression patterns

	Slice-time profiles (T, APT, DVT, LRT) - These are generated by slicing the embryo along one axis, and showing the average of each slice over time. DVT and LRT refer to slicing along the dorsal-ventral and left-right axes, respectively.
	XYZ profiles - These are generated by superimposing a cube on the embryo, and splitting it along the X, Y and Z axis. Effectively, the embryo is divided into voxels, and the average of each is shown over time.

The raw comparison metrics and clusterings are available as XML-files. These are not meant for reading, but rather provide a base for further calculations.

C. elegans models with expression patterns

Quick Endrov tutorial. This just highlights some of the most basic features of the software; it is not meant as a full instruction. Further instructions and the software is available at www.endrov.net.

To open a dataset below, you first have to unzip it. Then, in Endrov, you should NOT double-click the OST-file in the open dialog but just select the directory, then press the "open"-button.

All single-cell (SC) expression patterns on the model (C. elegans 2008). The APT profiles are also included as a separate lineage, although they might be easier to view using the summary figures above.

Comparison with microarray data

The T-profiles plotted against microarrays of staged embryos. Available both as PDFs and as a lineage in an OST-file (for viewing in Endrov). The microarray dataset (GSE15234) is taken from:

Yanai I, Hunter CP. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved.
Genome Res 2009 Dec;19(12):2214-20. PMID: 19745112

Original image data

The data is too large for a simple upload; please contact us to gain access

Citing

See paper here