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Volume 2012 (2012), Article ID 937506, 13 pages
Genes Regulated in Metastatic Osteosarcoma: Evaluation by Microarray Analysis in Four Human and Two Mouse Cell Line Systems
Laboratory for Orthopedic Research, Balgrist University Hospital, Forchstrasse 340, 8008 Zurich, Switzerland
Received 6 July 2012; Accepted 7 September 2012
Academic Editor: Norman Jaffe
Copyright © 2012 Roman Muff 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 Figure S1: (a) Distribution of mean log2 gene expression levels in SAOS/LM5 system. (b) Distribution of mean log2 gene expression levels in Dunn/LM8 system.
Supplementary Figure S2: Quantification of gene expression by real-time PCR in SAOS (open bars) and LM5 (black bars) cells. (a) Up-regulated and (b) down-regulated genes in metastatic LM5 cells compared to non-metastatic parental SAOS cells. GAPDH was used as a reference gene.
Supplementary Figure S3: Top network identified by Ingenuity Pathway analysis after analysis of 48 commonly regulated genes in SAOS/LM5 and Dunn/LM8 cell systems. Red indicates down-regulation (fold change >2, fdr < 0.01) in both cell systems, green indicates up-regulation, with the color intensity indicating the degree of up- or down-regulation.
Supplementary Table S1: PCR primers used for validation of microarray data, shown in Supplementary Figure S2.
Supplementary Table S2: Number of regulated (>2-fold; fdr < 0.01) probe sets enriched (fdr < 0.00001) in GO analysis at levels higher than 1, but with significant nodes down to level 1.
Supplementary Table S3: Ranking of top bio functions following IPA analysis. For each cell system, a cut-off was chosen such that comparable amounts of molecules were analyzed (in MG63/M8, a lower number of probe sets -521- were found to be significantly regulated, corresponding to a lower number -364- of recognized molecules). The top-5 bio functions, divided into the subcategories “diseases and disorders”, “molecular and cellular function” and “physiological system development and function” were compared among cell systems with the order displayed. Functions that were most commonly observed are shown first for each subcategory.
Supplementary Table S4: GO terms commonly up- or down-regulated in metastasis in the SAOS/LM5 and Dunn/LM8 cell line systems.