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Open Access Highly Accessed Research article

A systems biology approach reveals common metastatic pathways in osteosarcoma

Ricardo J Flores12, Yiting Li12, Alexander Yu12, Jianhe Shen12, Pulivarthi H Rao12, Serrine S Lau4, Marina Vannucci5, Ching C Lau123 and Tsz-Kwong Man123*

Author Affiliations

1 Texas Children’s Cancer and Hematology Centers, Texas Children’s Hospital, Houston, TX, USA

2 Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA

3 Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA

4 Southwest Environmental Health Science Centers, The University of Arizona, Tucson, AZ, USA

5 Department of Statistics, Rice University, Houston, TX, USA

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BMC Systems Biology 2012, 6:50  doi:10.1186/1752-0509-6-50

Published: 28 May 2012

Additional files

Additional file 1:

Table S1. Significant Pathways from the ontology enrichment of the down-regulated genes in the HOS/143B model and SaOS-2/LM7 model. Tables S2a and S2b. “Cytoskeleton remodeling/TGF/WNT” pathway proteins up-regulated in the RPPA on HOS/143B and SaOS-2/LM7 models.

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Additional file 2:

Figure S1. Pathway analysis of all glycogenes. Top significant pathways identified by MetaCore using all 191 glycogenes identified in the genomic profile. All pathways shown are significant. Refer to Figure 1 legend for graph details.

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Additional file 3:

Figure S2. Pathway analysis of differentially regulated glycogenes from 143B/HOS and LM7/SaOS-2 models. Top significant pathways identified by MetaCore using (a) differentially regulated genes from 143B/HOS model, and (b) differentially regulated genes from LM7/SaOS-2 model. Results showed that “N-Glycan biosynthesis” was the top common pathway between the two models. Dark orange bars represent significant pathways. Refer to Figure 1 legend for graph details.

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Additional file 4:

Methods for the N-Linked glycoproteins enrichment by lectin affinity chromatography.

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Additional file 5:

Figure S3. Pathway analysis of random genes and their topological nodes. Top significant pathways identified by MetaCore using (a) 300 randomly selected genes and (b) topological significant nodes from the 300 randomly selected genes. None of the top common significant pathways identified from the topological analysis of the up-regulated genes and up-regulated glycoproteins from the 143B/HOS and LM7/SaOS-2 models were identified by the topological analysis of this random gene set. Dark orange bars represent significant pathways. Refer to Figure 1 legend for graph details.

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