Fig. 3. Gene expression analysis. Gene expression changes between ectodermal and mesendodermal cells. Wild-type embryos consisting of both ectodermal and mesendodermal cells were compared with samples of ectodermal or mesendodermal cells using Affymetrix zebrafish gene arrays in triplicate. (A) The 220 most significantly regulated genes were selected based on an expected false discovery rate (FDR) of 5%. After centering and normalizing, the genes were clustered according to their regulation pattern. Color coding: up-regulated, red; unchanged, black; downregulated, green. (B) The regulation factor comparing mesendodermal with ectodermal cells on a transcriptional level was plotted against the regulation factor of 2D gel spot intensities. Areas of regulation in the same direction are shaded gray. The overall correlation between gene expression and spot intensity is weak.