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A matrix rank based concordance index for evaluating and detecting conditional specific co-expressed gene modules.
- Source :
- BMC Genomics; 8/22/2016, Vol. 17, p303-315, 13p, 1 Diagram, 1 Chart, 5 Graphs
- Publication Year :
- 2016
-
Abstract
- Background: Gene co-expression network analysis (GCNA) is widely adopted in bioinformatics and biomedical research with applications such as gene function prediction, protein-protein interaction inference, disease markers identification, and copy number variance discovery. Currently there is a lack of rigorous analysis on the mathematical condition for which the co-expressed gene module should satisfy. Methods: In this paper, we present a linear algebraic based Centralized Concordance Index (CCI) for evaluating the concordance of co-expressed gene modules from gene co-expression network analysis. The CCI can be used to evaluate the performance for co-expression network analysis algorithms as well as for detecting condition specific co-expression modules. We applied CCI in detecting lung tumor specific gene modules. Results and Discussion: Simulation showed that CCI is a robust indicator for evaluating the concordance of a group of co-expressed genes. The application to lung cancer datasets revealed interesting potential tumor specific genetic alterations including CNVs and even hints for gene-fusion. Deeper analysis required for understanding the molecular mechanisms of all such condition specific co-expression relationships. Conclusion: The CCI can be used to evaluate the performance for co-expression network analysis algorithms as well as for detecting condition specific co-expression modules. It is shown to be more robust to outliers and interfering modules than density based on Pearson correlation coefficients. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 17
- Database :
- Complementary Index
- Journal :
- BMC Genomics
- Publication Type :
- Academic Journal
- Accession number :
- 117641229
- Full Text :
- https://doi.org/10.1186/s12864-016-2912-y