Open Access Research article

A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study

Elena Fountzilas1, Andrew D Kelly1, Antonio R Perez-Atayde4, Jeffrey Goldsmith2, Panagiotis A Konstantinopoulos1, Nancy Francoeur1, Mick Correll3, Renee Rubio3, Lan Hu3, Mark C Gebhardt5, John Quackenbush3 and Dimitrios Spentzos1*

Author Affiliations

1 Division of Hematology/Oncology, Sarcoma Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA

2 Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA

3 Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA

4 Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02215, USA

5 Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA

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BMC Genomics 2012, 13:332  doi:10.1186/1471-2164-13-332

Published: 23 July 2012

Additional files

Additional file 1:

Table S1. Commonly activated and silenced miRNAs across all sarcoma histological subtypes. A superscript 1 denotes miRNAs with potential sequence alterations. Table S2. miRNA activity patterns in osteosarcoma. Osteosarcoma-specific deregulation patterns compared to all normal tissue (p = 0.005 and FDR = 0.01). Table S3. miRNA activity patterns in osteosarcoma. Osteosarcoma-specific deregulation patterns compared to mesenchymal normal tissue (p = 0.005 and FDR = 0.01). Table S4. miRNAs commonly activated or silenced in sarcomas and epithelial cancers. Table S5. miRNAs deregulated in the “RAS active” group (p = 0.005 and FDR = 0.01). Table S6. miRNAs deregulated in the “RAS non-active” group (p = 0.005 and FDR = 0.01). Table S7. RAS-switching miRNAs by sarcoma histological subtype. Boldface denotes miRNAs which overlap with those identified in the aggregate RAS pathway analysis. Table S8. Biological themes represented in distinct miRNA activity patterns. Boldface denotes the pathways discussed in the main text of the manuscript.

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