Additional file 1:

List of differentially expressed genes. Genes numbered from 1 to 554 (column A) passed both statistical analyses (SAM and "intensity-dependent calculation of standard Z-score", see Methods), those numbered from 555 to 993 passed only the SAM analysis. The other columns show: (B) the OPERON oligo ID in the OMAD database [50]; (C) the EntrezGene ID; (D) the Gene Symbol; (E) the description of the gene ; (F) genes belonging to the cluster of interacting genes in Figure 3, marked "1"; (G-L) genes up-regulated in cells treated with TGFβ1 have log² values higher than 0, genes down-regulated have values lower than 0 (values that passed the statistical analysis are in bold); (M) genes up-regulated in the plastic substrate by comparison with the collagen type I have values higher than 0, genes down-regulated have values lower than 0; (N) geometric means of the experiments in columns (G-L).

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Additional file 2:

KEGG analysis of differentially expressed genes. 267 genes in Additional file 1 with an EntrezGene ID were placed in the KEGG maps using the "color genes" option in the KEGG database [41]. Differentially expressed genes that only passed the SAM analysis were colored orange (up-regulated) and light-blue (down-regulated); genes that passed both statistical analyses (see Methods) were colored red (up-regulated) and blue (down-regulated).

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