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BioMed Research International
Volume 2014, Article ID 840921, 8 pages
Research Article

Analysis of Differential miRNA Expression in Primary Tumor and Stroma of Colorectal Cancer Patients

1Department of Clinical Medicine and Surgery, University Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
2Department of Biology, University of Padova, Via 8 Febbraio 2, 35122 Padova, Italy
3Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
4Department of Public Health, University Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
5Department of Medicine, University of Salerno, Via Salvatore Allende 43, 84084 Baronissi, Italy

Received 27 February 2014; Revised 13 May 2014; Accepted 27 May 2014; Published 10 July 2014

Academic Editor: Kostas Iatrou

Copyright © 2014 Giuseppina Della Vittoria Scarpati et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Supplementary Figure 1. Bootstrap hierarchical clustering of normalized data passing the QC filter (321 microRNAs). Each column represents a sample (T, tumor; S, stroma). The red branches in the dendrogram indicate an approximately unbiased (AU) confidence level greater than 95%.

Supplementary Figure 2. Heatmap and bootstrap hierarchical clustering of differentially expressed microRNA in tumor versus stroma comparisons. Each row represents a single microRNA, and each column a matched tumor sample (T) versus stromal sample (S) comparison. Green colors indicate down-regulation (negative log fold change), while red colors indicate up-regulation (positive fold change). The red branches in the dendrograms indicate an approximately unbiased (AU) confidence greater than 95%.

Supplementary Table 1. Complete list of differentially expressed miRNA between tumor and matched stroma samples. ID, official miRNA name according to miRBASE version 19; logFC , log2 fold change of tumor expression versus stroma (negative for down-regulated miRNA and positive for up-regulated miRNA); p-value, the raw p-value from the statistical test; adjusted p-value, the p-value from the statistical test adjusted for multiple test comparisons (False Discovery Rate).

Supplementary Table 2: Number of validated targets, pathway enrichment of validated target and known association of differentially expressed miRNAs to colorectal cancer.

Supplementary Table 3. RT-PCR and microarray analysis of the 13 DE miRNA selected in tumor and matched stroma samples. All data are median distribution (IQ-range:2.5-97.5 percentile) of fluorescence intensity, normalized as described in the Methods section. R, the ratio of the median distribution of tumor to stroma samples measured by RT-PCR; P, the level of significance according to the Wilcoxon Rank test. Ra, the fold change (ratio) between tumor and stromal samples from the array analysis (in natural scale); q, the corrected p-value (q-value) from the array analysis.

  1. Supplementary Material