CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

Overview

Journal Gene Regul Syst Bio

Publisher Sage Publications

Date 2009 Nov 26

PMID 19936083

Citations 1

Authors

Joyce Xiuweu-Xu Gu

Michael Yang Wei

Pulivarthi H Rao

Ching C Lau

Sanjiv Behl

Tsz-Kwong Man

Affiliations

Soon will be listed here.

Abstract

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

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References

Kingsley C, Kuo W, Polikoff D, Berchuck A, Gray J, Jain A . Magellan: a web based system for the integrated analysis of heterogeneous biological data and annotations; application to DNA copy number and expression data in ovarian cancer. Cancer Inform. 2009; 2:10-21. PMC: 2675496. View

Margolin A, Greshock J, Naylor T, Mosse Y, Maris J, Bignell G . CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics. 2005; 21(15):3308-11. DOI: 10.1093/bioinformatics/bti500. View

Saraiya P, North C, Duca K . An insight-based methodology for evaluating bioinformatics visualizations. IEEE Trans Vis Comput Graph. 2005; 11(4):443-56. DOI: 10.1109/TVCG.2005.53. View

Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N . TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003; 34(2):374-8. DOI: 10.2144/03342mt01. View

Man T, Chintagumpala M, Visvanathan J, Shen J, Perlaky L, Hicks J . Expression profiles of osteosarcoma that can predict response to chemotherapy. Cancer Res. 2005; 65(18):8142-50. DOI: 10.1158/0008-5472.CAN-05-0985. View

Jong K, Marchiori E, Meijer G, Vaart A, Ylstra B . Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics. 2004; 20(18):3636-7. DOI: 10.1093/bioinformatics/bth355. View

Cheung S, Shaw C, Yu W, Li J, Ou Z, Patel A . Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet Med. 2005; 7(6):422-32. DOI: 10.1097/01.gim.0000170992.63691.32. View

Chen W, Erdogan F, Ropers H, Lenzner S, Ullmann R . CGHPRO -- a comprehensive data analysis tool for array CGH. BMC Bioinformatics. 2005; 6:85. PMC: 1274268. DOI: 10.1186/1471-2105-6-85. View

Bumm K, Zheng M, Bailey C, Zhan F, Chiriva-Internati M, Eddlemon P . CGO: utilizing and integrating gene expression microarray data in clinical research and data management. Bioinformatics. 2002; 18(2):327-8. DOI: 10.1093/bioinformatics/18.2.327. View

10.

Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D . High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998; 20(2):207-11. DOI: 10.1038/2524. View

11.

Li C, Wong W . Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A. 2001; 98(1):31-6. PMC: 14539. DOI: 10.1073/pnas.98.1.31. View

12.

Shankar G, Rossi M, McQuaid D, Conroy J, Gaile D, Cowell J . aCGHViewer: a generic visualization tool for aCGH data. Cancer Inform. 2007; 2:36-43. PMC: 1847423. View

13.

Kim S, Nam S, Lee S, Park W, Yoo N, Lee J . ArrayCyGHt: a web application for analysis and visualization of array-CGH data. Bioinformatics. 2005; 21(10):2554-5. DOI: 10.1093/bioinformatics/bti357. View

14.

Price T, Regan R, Mott R, Hedman A, Honey B, Daniels R . SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res. 2005; 33(11):3455-64. PMC: 1151590. DOI: 10.1093/nar/gki643. View

15.

Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R . EXPANDER--an integrative program suite for microarray data analysis. BMC Bioinformatics. 2005; 6:232. PMC: 1261157. DOI: 10.1186/1471-2105-6-232. View

16.

Attar R, Gilman M . Expression cloning of a novel zinc finger protein that binds to the c-fos serum response element. Mol Cell Biol. 1992; 12(5):2432-43. PMC: 364416. DOI: 10.1128/mcb.12.5.2432-2443.1992. View

17.

Sykacek P, Furlong R, Micklem G . A friendly statistics package for microarray analysis. Bioinformatics. 2005; 21(21):4069-70. DOI: 10.1093/bioinformatics/bti663. View

18.

Man T, Lu X, Jaeweon K, Perlaky L, Harris C, Shah S . Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma. BMC Cancer. 2004; 4:45. PMC: 514550. DOI: 10.1186/1471-2407-4-45. View

19.

Vaquerizas J, Conde L, Yankilevich P, Cabezon A, Minguez P, Diaz-Uriarte R . GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res. 2005; 33(Web Server issue):W616-20. PMC: 1160260. DOI: 10.1093/nar/gki500. View