Reconstruction of Gastrulation from a murine ES cells differentiation Microarray data

Reconstruction of Gastrulation from a murine ES cells differentiation Microarray data


Gastrulation is a phase in early animal embryo development. During this phase the three germ layers develop and the embryo is dramatically restructured by cell migration. The three germ layers the develop into certainly body systems:

  • The endoderm mainly develops into the Gastrointestinal tract, the Respiratory tract, and the Endocrine glands and organs (liver and pancreas).
  • The mesoderm maily develops into the somites, the notochord, and the mesenchyme, which give rise to the muscles, circulatory and excretory systems of the body.
  • The ectoderm develops into the skin, nails, the epithelium of the nose, mouth and anal canal.

The formation of the germ layers is attended by specific gene expression patterns measured using microarrays.

The dataset

The datasert consists of three mES cell lines (R1,J1,V6.5) differentiated into embrioid bodies which are aggregates of cells derived from embryonic stem cells. Thereby the aggregates recapitulate to a limited extent the embryonic develpment of an organism.

RNA was extracted at 11 time points from each cell line. The microarray datasets are available from the GEO repository ( with the series accesion identifiers GSE2972, GSE3749, and GSE3231, respectively.

The task and evaluation criteria

Although the detailed genetic mechanisms are only partially understood, many developmantal genes are assiciated with the differentiation of one or more of the three germ layers. The task is to reconstruct the gene expression patterns responsible for the formation of the three germ layers from the microarray data using blind source separation techniques. As an underlying model we'd suppose a linear factor model as described in Lutter et al. BMC Bioinformatics, 2008, and Teschendorff et al. PLoS CB, 2007.

Evaluation of the results will be done with Medical Subject Headings (MeSH) term associated gene lists. The gene lists will be provided here soon.

Potential participants

Florian Bloechl
Andreas Kowarsch

Task proposed by Biomedical/BCI Committee