Additional data file 9.

(A,B) Pairwise comparison (BMP2 versus control EBs): 2,258 probeset IDs that were differentially expressed in BMP2+ cells compared to control EBs (two-condition comparison) were converted to GenBank accession numbers and redundancies were removed (1,833 unique transcripts). Stanford Source was used to obtain GO biological process (BP) annotations. Genesis 1.7.0 was used to visualize and identify GO BP categories of interest and extract corresponding lists of transcripts. For the categories adhesion, cell cycle, cell death, cell-cell signaling, cellular metabolism, development, stress response, signal transduction, transcription and transport, 1,541 annotations were established for 1,172 transcripts. The pie chart (A) shows the distribution of these annotations. The bar chart (B) shows the number of genes in the categories adhesion, cell cycle, cell death, cell-cell signaling, cellular metabolism, development, stress response, signal transduction, transcription and transport separately for up- and downregulated transcripts. (C,D) Three-condition comparison (BMP2 versus control EBs and BMP2 ES cells). For the three-condition comparison, 551 unique transcripts were obtained from 672 probeset IDs that were differentially expressed in BMP2 versus control EBs and versus undifferentiated BMP2 ES cells using the approach described above. For the categories adhesion, cell cycle, cell death, cell-cell signaling, cellular metabolism, development, stress response, signal transduction, transcription and transport, 430 annotations were established for 268 transcripts. The pie chart (C) shows the distribution of these annotations. The bar chart (D) shows the number of genes in the categories adhesion, cell cycle, cell death, cell-cell signaling, cellular metabolism, development, stress response, signal transduction, transcription and transport separately for up- and downregulated transcripts. (E) Clustering analysis of the probesets identified as differentially expressed in the two-condition comparison (see A) and assigned to the GO category 'development'. Expression data were normalized using the RMA algorithm and hierarchical clustering was done using Cluster 2.11 as described. Visualization of the hierarchical clustering of probe sets identified as differentially expressed in the pairwise comparison (see A) and assigned to the GO category 'development'. Each probe set is represented by a single column of colored boxes; each array is represented by a single row. Cells with unchanged probe sets are colored black, upregulation is indicated with reds of increasing intensity, and downregulation with greens of increasing intensity. The dendrogram on the top of the figure represents the similarity matrix of probe sets, the dendrogram to the right the similarity matrix of arrays.

Format: PDF Size: 85KB Download file

This file can be viewed with: Adobe Acrobat Reader

Doss et al. Genome Biology 2007 8:R184   doi:10.1186/gb-2007-8-9-r184