Figure 2

Gene clustering by self-organizing maps (SOM) (a, b) and literature-profiling (b). (a) Genes clustered according to their expression dynamics (SOM): twenty-four clusters were disclosed by the SOMs algorithm, which were grouped into 6 patterns, i.e.: (1) genes transiently upregulated in the acute phase (yellowish); (2) genes continuously upregulated in the acute and the late phase (reddish); (3) genes transiently downregulated in the acute phase (bluish); (4) genes continuously downregulated in the acute and the late phase (greenish); (5) genes transiently upregulated in CX and continuously upregulated in HC (black); (6) genes transiently downregulated in CX and continuously upregulated in HC (brown). Patterns 1, 2 and 3 are subdivided into "mega-clusters" comprising clusters of genes differentially regulated only in CX, or only in HC, or in both tissues concomitantly. Pattern 4 contained two clusters, one with genes continuously downregulated only in CX, the other with genes continuously downregulated only in HC. In each cluster diagram, the three points on the left side represent the average gene expression levels in the CX in mock-infected animals, and in infected animals in the acute and the late phase, respectively. The three points on the right side refer to gene expression in the HC at these time points. cn is the identification of each cluster, and the following values correspond to the number of probe-sets comprising the cluster. Clusters c4, c5, c6, c7, c10, c11, c14, c15, c18 and c21 contain 227 probe-sets representing genes with a similar gene expression pattern in CX and HC; Clusters c8, c9, c12, c19, c22 and c23 contain 157 probe-sets representing genes differentially regulated only in the CX; Clusters c0, c1, c2, c3, c13, c16 and c17 contain 214 probe-sets representing genes differentially regulated only in the HC. (b) Combined clustering obtained with self-organizing maps and literature-profiling: Cold colors (bluish and greenish) represent genes that were downregulated, and warm colors (yellowish and reddish) represent genes that were upregulated. The corresponding clusters disclosed by the SOM algorithm are indicated in the box, following the same color schema of Figure 3(a). Detached pieces in the pies represent genes differentially regulated only in the HC.