2 PDZ domain containing RING finger 3 PDZRN3 Protein ubiquitination SBE-��-CD concentration chr3p21.1 -58% -8.9 TU3A protein TU3A Regulation of cell growth chr14q32.1 -48% -8.5 serine proteinase inhibitor, clade A, member 5 SERPINA5 Endopeptidase inhibitor chr3p22-p21.3 -58% -8.5 C-type lectin domain family 3, member B CLEC3B Skeletal development chr9p13.2-p13.1 -42% -8.3 tropomyosin 2 TPM2 Muscle development

chr14q32 -48% -8.1 delta-like 1 homolog DLK1 Calcium ion binding chr6q27 -58% -6.5 ribosomal protein S6 kinase, 90 kDa, polypeptide 2 RPS6KA2 Amino acid phosphorylation chr6q24-q25 -52% -6.2 pleiomorphic adenoma gene-like 1 PLAGL1 Regulation of transcription chr9p13-p12 -42% -5.8 reversion-inducing-cysteine-rich protein with kazal motifs RECK Cell cycle regulation chr3p21.2-p21.1 -61% -5.4 aminomethyltransferase AMT Glycine catabolism chr6pter-qter -48% -5.4 transcription factor 21 TCF21 Regulation of transcription chr9q13 -42% -5.1 Kruppel-like factor 9 KLF9 Regulation of transcription chr6q23 -48% -3.8 serum/glucocorticoid regulated kinase SGK Amino acid phosphorylation chr3p26-p25 -45% -3.6 inositol 1,4,5-triphosphate receptor, type 1 ITPR1 Cell cycle regulation chr1p36.13-p36.11 -55% -3.2 neuroblastoma, suppression of tumorigenicity 1 NBL1 calcium ion transport chr6q22 -55% -2.6 mannosidase, alpha,

class 1A, member 1 MAN1A1 Carbohydrate metabolism chr3p22 -48% -2.5 transforming growth factor, beta receptor II TGFBR2 Regulation of cell proliferation Validation of Findings The Affymetrix U133A gene expression array data were both buy LY411575 internally and externally validated. First, a large number of gene transcripts were represented by more than one probe set in the array. In each case, the different probes for each detected similar expression levels of transcript (See additional files 1, additional file 2, and additional file 3). This includes genes with Epacadostat altered expression in EHC (i.e. CDKN1C, NR4A3, RBM5, SASH1), IHC (ADH1B, GREM1, MCM4, NR4A2), and GBC (HIST2H2AA, NUSAP1 RPS10, RPS19). In addition, to externally validate our data, selected differentially

expressed genes were measured for transcript levels in biliary carcinoma specimens and in normal biliary epithelial controls using quantitative reverse transcriptase PCR. We assayed 11 genes with differing biologic functions and involvement Dipeptidyl peptidase in diverse molecular pathways but with known importance in carcinogenesis. These included genes which were overexpressed in EHC (SRDA21, STAT1, UBD, TYMS), underexpressed in EHC (FOSB, CDKN1C, IL6), overexpressed in IHC (SRDA21, STAT1, UBD, TYMS), underexpressed in IHC (DLC1, NR4A2, IL6), and overexpressed in GBC (UBD, TYMS, CDC2, CCNB2). PCR data was normalized to HPRT which was expressed at similar levels in both the cancerous and the control biliary epithelium (not shown). Results are shown in Figures (3a–f, 4g–k) and, for each gene tested, confirm the Affymetrix U133A gene expression array data.