BMC Genomics 2005, 6:130 http://www.biomedcentral.com/1471-2164/6/130 FAi)gCuorem1parison of most expressed tags among different SAGE libraries A) Comparison of most expressed tags among different SAGE libraries. Normalized expression levels (TPM) are similar between libraries with different total sequenced tags, indicating comparable messenger abundance among top expressed genes. Expression levels were obtained from SAGEmap website http://wwwncbinlmnihgov/projects/SAGE/index cgi?cmd=expsetup. aTPM: Tags per million. Normalization to compare libraries with different numbers of sequenced tags. TPM is obtained by the following formula [(Tag frequency)(1000,000)/Total No. of sequenced tags]. bDN: digital northern, indicating gene expression level for a specific gene in a library. B. Graphical representation of expression levels (TPM) for three constitutive genes in several normal (N) and tumoral (T) tissues. Brain tissue libraries: SAGE BB542 whitematter (N) and SAGE Brain medulloblastoma B 98 04 P117 (T). Breast: SAGE Breast normal organoid (N) and B SAGE Breast carcinoma epithelium AP DCIS6 (T). Gastric: SAGE normal gastric body epithelial (N) and SAGE Hiroshima GC W246T (T). Liver: SAGE normal liver (N) and SAGE Liver cholangiocarcinoma B K2D (T). Kidney: SAGE Duke Kidney (N) and SAGE_Kidney_carcinoma_B_D2 (T). Colon: SAGE NC2 (N) and SAGE Tu98 (T). Prostate: SAGE PR317 normal prostate (N) SAGE PR317 prostate tumor (T). Lung: SAGE normal lung (N) and SAGE Lung adenocarcinoma MD L10 (T). Expression levels are indicated as tags per million. differentiation stages (basale, spinosum and granulosum strata). Nevertheless, these tissues also contain fibroblasts associated with connective, besides other minor cell pop- ulations. To know which genes are related to fibroblasts, we compared a SAGE library derived from neonatal fore- skin primary fibroblasts (Agnes Baross, British Columbia Genome Sciences Centre). We found 923 gene tags shared by both libraries, which could due to the presence of fibroblasts in the Cervix SAGE library (supplementary information). Shared genes with known biological func- tion reveal that processes as signal transduction, regula- tion of transcription and cell adhesion are mainly involved. We consider important to identify minor contri- butions to global gene expression profile in a heterogene- ous cell population; however, it is important to note that unknown differences between cervical and neonatal fore- skin fibroblasts could exist. Page 4 of 9 (page number not for citation purposes)