Joly et al. BMC Genomics 2010, 11:422 http://www.biomedcentral.com/1471-2164/11/422 Page 6 of 16 Figure 2 Serial analysis of gene expression: stage-specificity of putative secretome members of the Melampsora unisequence dataset. Similarities in serial analysis of gene expression (SAGE) patterns of 182 putative secretome members of the Melampsora unisequence dataset were determined using an average linkage hierarchical clustering according to the Spearman Rank Correlation. Corresponding tags were identified as described in the Methods section. Each row represents a tag, whereas each column corresponds to a SAGE library. 22H_C: 22 hours after inoculation (compatible interaction); 22H_I: 22 hours after inoculation (incompatible interaction); 2H: 2 hours after inoculation (germinating spores); 5D_C: 5 days after inoculation (compatible interaction); and 5D_I: 5 days after inoculation (incompatible interaction). Genes upregulated during the biotrophic or pre-biotrophic stages are highlighted in blue and yellow, respectively. Medium blue = genes specific to the biotrophic stage; Light blue = genes upregulated during the biotrophic stage; Dark yellow = genes upregulated in 22H_I; Medium yellow = genes upregulated in 22H_C; and Light yellow = genes upregulated in 2 H. The relative abundance of the SAGE tag in the library correlates with the intensity of the red color (black, not present; intense red, highly abundant). Brackets indicate clades containing homologues of haustorially expressed secreted proteins (HESPs) 735, 417, and 379, respectively. expression patterns were consistent with observations made in our libraries, with 60% of the represented haus- torium-enriched library unisequences being upregulated during the biotrophic stage. Compatible and incompati- ble treatments were grouped together at each time point, and the pre-biotrophic stage libraries were clus- tered together and separated from the biotrophic stage libraries. Even though similar stage specificity has been observed for the non-secreted counterpart (data not shown), the abundance of tags pointed towards higher expression levels for secreted proteins during the pre- biotrophic stage when compared to the rest of the tran- scriptome. On the other hand, secretome members found during the biotrophic stage had expression levels similar to their non-secreted counterpart (Additional File 3). The mean number of tags per unisequences cor- related well with the abundance of clones per contig. While the haustorium-enriched library shared a