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Open Access Methodology article

Semi-supervised discovery of differential genes

Shigeyuki Oba* and Shin lshii

Author Affiliations

Graduate School of Information Science, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan

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BMC Bioinformatics 2006, 7:414  doi:10.1186/1471-2105-7-414

Published: 18 September 2006

Abstract

Background

Various statistical scores have been proposed for evaluating the significance of genes that may exhibit differential expression between two or more controlled conditions. However, in many clinical studies to detect clinical marker genes for example, the conditions have not necessarily been controlled well, thus condition labels are sometimes hard to obtain due to physical, financial, and time costs. In such a situation, we can consider an unsupervised case where labels are not available or a semi-supervised case where labels are available for a part of the whole sample set, rather than a well-studied supervised case where all samples have their labels.

Results

We assume a latent variable model for the expression of active genes and apply the optimal discovery procedure (ODP) proposed by Storey (2005) to the model. Our latent variable model allows gene significance scores to be applied to unsupervised and semi-supervised cases. The ODP framework improves detectability by sharing the estimated parameters of null and alternative models of multiple tests over multiple genes. A theoretical consideration leads to two different interpretations of the latent variable, i.e., it only implicitly affects the alternative model through the model parameters, or it is explicitly included in the alternative model, so that the interpretations correspond to two different implementations of ODP. By comparing the two implementations through experiments with simulation data, we have found that sharing the latent variable estimation is effective for increasing the detectability of truly active genes. We also show that the unsupervised and semi-supervised rating of genes, which takes into account the samples without condition labels, can improve detection of active genes in real gene discovery problems.

Conclusion

The experimental results indicate that the ODP framework is effective for hypotheses including latent variables and is further improved by sharing the estimations of hidden variables over multiple tests.