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Open Access Methodology article

Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior

Lam C Tsoi1, Tingting Qin1, Elizabeth H Slate2 and W Jim Zheng3*

Author Affiliations

1 Bioinformatics Graduate Program, Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 135 Cannon St. Charleston, SC 29425, USA

2 Department of Statistics, Florida State University, 117 N. Woodward Ave. Tallahassee, FL 32306, USA

3 Division of Bioinformatics, Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 135 Cannon St. Charleston, SC 29425, USA

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BMC Bioinformatics 2011, 12:438  doi:10.1186/1471-2105-12-438

Published: 11 November 2011

Additional files

Additional file 1:

Supplementary materials for the analysis. Detailed descriptions about: 1) Datasets Used (Suppl. Table 1); 2) The comparisons between p-values computed by the parametric t-test versus the non-parametric RankProd (Suppl. Figure 1); 3) The Bayesian mixture for the p-value distribution (Suppl. Figure 2, Table 2 and Table 3); 4) Comparisons of different approaches for handling genes appearing in different numbers of datasets based on simulation (Suppl. Figure 3, Figure 4, Figure 5 and 6); and 5) Comparisons of the three approaches using the 6 cancer datasets as case study (Suppl. Figure 7).

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Additional file 2:

Results from the simulation data. The statistical power and Type I error rate are compared for the three meta-analysis approaches on simulation data.

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Additional file 3:

Metastases-related genes identified by CDEP. Statistically significant genes identified by CDEP as related to metastatic behavior by using FDR = 0.05.

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Additional file 4:

Comparison of Significant Genes Identified by CDEP, Meta-Profile and Meta-RankProd. List of genes that are differentially expressed consistently in metastatic cancer cells as identified by CDEP, Meta-Profile and Meta-RankProd from six data sets used.

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