Open Access Highly Accessed Research article

Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer

Meng Li1, Curt Balch123, John S Montgomery1, Mikyoung Jeong4, Jae Hoon Chung4, Pearlly Yan5, Tim HM Huang5, Sun Kim67* and Kenneth P Nephew1238*

Author Affiliations

1 Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA

2 Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA

3 Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA

4 Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Taejon 305-701, South Korea

5 Division of Human Cancer Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA

6 School of Informatics, Indiana University, Bloomington, IN 47405, USA

7 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47404, USA

8 Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis 46202, USA

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BMC Medical Genomics 2009, 2:34  doi:10.1186/1755-8794-2-34

Published: 8 June 2009

Additional files

Additional file 1:

Agilent annotation file for the customized 44 K promoter CpG island array. The annotation file includes detailed information for microarray chip set-up and probe design for the customized 44 K promoter CpG island array used in the DMH experiment.

Format: CSV Size: 13.9MB Download file

Open Data

Additional file 2:

Hierarchical clustering of the 3127 significantly up- or down-regulated probes in Round5. The figure shows the clustering results with gene tree and probe names included of all significantly altered probes in Round5 vs. parental A2780 cells.

Format: PNG Size: 665KB Download file

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Additional file 3:

Differentially expressed genes and probes in Round5 vs. parental A2780 cells. The table lists all 2322 significantly differentially expressed genes, sorted by their average fold-changes, in Round5 vs. parental A2780 cells.

Format: XLS Size: 659KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

Functional clustering analysis of all 1036 genes upregulated in Round5. The table shows the functional annotation clustering analysis results of the upregulated genes in Round5 by DAVID. Functional annotation groups with geometric p-value less than 0.05 are listed. Each functional group contains related annotation terms that represent similar biological functions.

Format: XLS Size: 58KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 5:

Functional clustering analysis of all 1286 genes downregulated in Round5. The table shows the functional annotation clustering analysis results of the downregulated genes in Round5 by DAVID. Functional annotation groups with geometric p-value less than 0.05 are listed. Each functional group contains related annotation terms that represent similar biological functions.

Format: XLS Size: 39KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data