For increased confidence, we repeated each microarray assay twice. The scatter diagrams and correlation assessment of all spots showed that the reproducibility and reliability were good (Figure 2). The supervised cluster analysis, based on differentially expressed miRNAs, generated a tree

with clear distinction between cancerous and normal tissues (Figure 3). Table 2 MicroRNAs microarray SAM results and correlation with cancer microRNA Name Fold Change Type Numerator (r) Denominator (s+s0) Correlation with cancer squamous cell carcinoma vs normal cheek pouch tissue hsa-miR-21 2.590 up 2.495 1.371 Up-regulated in glioblastomas[11], breast[8], colon[7], lung[9], pancreatic[17], thyroid[10], and Selleck FK506 ovarian cancer[15] hsa-miR-200b 2.192 up 1.645 0.964 Up-regulated in ovarian cancer[15] hsa-miR-221 2.018 up 1.561 0.988 Up-regulated in CLL[8], glioblastomas[11], thyroid[10], Ro 61-8048 mw and pancreatic cancer[17] hsa-miR-338 2.436 up 1.323 0.493   mmu-miR-762 2.379 up 1.863 1.052   hsa-miR-16 0.182 down -2.501 0.458 Down-regulated in CLL[8], and prostate cancer[12]

SP600125 hsa-miR-26a 0.135 down -2.288 1.148 Down-regulated in prostate[12], and ovarian cancer[15] hsa-miR-29a 0.245 down -1.532 0.785 Down-regulated in ovarian cancer[15] hsa-miR-124a 0.216 down -1.819 0.702 Down-regulated in colon[7], breast[8] and lung cancer[9] hsa-miR-125b 0.414 down -1.282 0.418 Down-regulated in breast[8], lung[9], ovarian[15], cervical[16], and prostate cancer[12] mmu-miR-126-5p 0.424 down -1.117 0.536   hsa-miR-143 0.393 down -1.245 PRKD3 0.605 Down-regulated in prostate[12], Lung[9], breast[8], hepatocellular[14], colon[7], cervical[16], and ovarian cancer[15] hsa-miR-145 0.317 down -2.130 0.899 Down-regulated in prostate[12], Lung[9], breast[8], hepatocellular[14], ovarian[15], cervical[16], and colon cancer[7] hsa-miR-148b 0.317 down -2.130 0.899 Down-regulated in pancreatic[17], and colon cancer[7] hsa-miR-155 0.376 down -1.374 0.486 Up-regulated in CLL[8], thyroid[10], lymphomas[13], lung[9], breast cancer[8] Down-regulated in pancreatic cancer[17] hsa-miR-199a 0.261 down -1.411

0.847 Down-regulated in prostate[12], and hepatocellular cancer[14] hsa-miR-203 0.175 down -1.925 0.910 Down-regulated in colon[7], and breast cancer[8] Up-regulated in ovarian cancer[15] CLL: chronic lymphocytic leukemia Figure 2 Experimental variation and reproducibility assessment from twelve microarray hybridizations in six different samples. Scatter diagram showing high reproducibility between the replicate experiments of every sample. The R-value in each microarray analysis showing that most of the average correlations are well above 0.9, indicating high reproducibility. Panel A~C: self-hybridization results obtained after probing the microarray with the same RNA sample prepared from three normal tissues and labeled separately with Cy3 dye.