Comprehensive evaluation of composite gene features in cancer outcome prediction

Cancer Informatics
Dezhi Hou, Mehmet Koyutürk

Abstract

Owing to the heterogeneous and continuously evolving nature of cancers, classifiers based on the expression of individual genes usually do not result in robust prediction of cancer outcome. As an alternative, composite gene features that combine functionally related genes have been proposed. It is expected that such features can be more robust and reproducible since they can capture the alterations in relevant biological processes as a whole and may be less sensitive to fluctuations in the expression of individual genes. Various algorithms have been developed for the identification of composite features and inference of composite gene feature activity, which all claim to improve the prediction accuracy. However, because of the limitations of test datasets incorporated by each individual study and inconsistent test procedures, the results of these studies are sometimes conflicting and unproducible. For this reason, it is difficult to have a comprehensive understanding of the prediction performance of composite gene features, particularly across different cancers, cancer subtypes, and cohorts. In this study, we implement various algorithms for the identification of composite gene features and their utilization in cancer outcome p...Continue Reading

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Citations

Sep 22, 2017·Nucleic Acids Research·Nicolas AlcarazJan Baumbach

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Datasets Mentioned

BETA
GSE7390
GSE6532
GSE17537
GSE2034
GSE17536

Methods Mentioned

BETA
Feature Selection
feature extraction
three hybrid

Software Mentioned

MATLAB
LinearPath2
NetCover
GreedyMI
LinearPathl
GreedyTtest
SVM

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