Open Access Highly Accessed Methodology article

Genome-wide identification of significant aberrations in cancer genome

Xiguo Yuan12, Guoqiang Yu23, Xuchu Hou2, Ie-Ming Shih48, Robert Clarke5, Junying Zhang1, Eric P Hoffman6, Roger R Wang7, Zhen Zhang8 and Yue Wang2*

  • * Corresponding author: Yue Wang yuewang@vt.edu

  • † Equal contributors

Author Affiliations

1 School of Computer Science and Technology, Xidian University, Xi'an, P. R. China

2 Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA

3 Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Palo Alto, CA, 94304, USA

4 Departments of Gynecology/Obstetrics and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA

5 Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC, 20057, USA

6 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC, 20010, USA

7 The International Baccalaureate Magnet Diploma Program, Richard Montgomery High School, Rockville, MD, 20852, USA

8 Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA

For all author emails, please log on.

BMC Genomics 2012, 13:342  doi:10.1186/1471-2164-13-342

Published: 27 July 2012

Additional files

Additional file 1:

Table S1. Comparative detection rates of ground truth SCA boundaries by STAC, GISTIC, KC-SMART, CMDS, and SAIC for simulation data sets under various model parameter settings. The results are calculated based on 100 replications for each of the parameter settings and using p-value (or q-value) cutoff threshold <0.05.

Format: DOC Size: 316KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

Table S2 and Table S3. Details about the implicated SCAs and full list of genes covered by these SCAs, derived from the ovarian cancer data set.

Format: DOC Size: 415KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

Table S4 and Table S5. Details about the implicated SCAs and full list of genes covered by these SCAs, derived from the prostate cancer data set.

Format: DOC Size: 402KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

Table 6 and Suplementary Table 7. Details about the implicated SCAs and full list of genes covered by these SCAs, derived from the lung adenocarcinoma data set.

Format: DOC Size: 282KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

Table S8 and Table S9. Details about the implicated SCAs and full list of genes covered by these SCAs, derived from the glioblastoma data set.

Format: DOC Size: 181KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data