Partially-independent component analysis for tissue heterogeneity correction in microarray gene expression analysis

Yue Wang, Junying Zhang, Javed Khan, Robert Clarke, Zhiping Gu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

Abstract

Gene microarray technologies provide powerful tools for the large scale analysis of gene expression in cancer research. Clinical applications often aim to facilitate a molecular classification of cancers based on discriminatory genes associated with different clinical stages or outcomes. However, gene expression profiles often represent a composite of more than one distinct source due to tissue heterogeneity, and could result in extracting signatures reflecting the proportion of stromal contamination in the sample, rather than underlying tumor biology. We therefore wish to introduce a computational approach which allows for a blind decomposition of gene expression profiles from mixed cell populations. The algorithm is based on a linear latent variable model, whose parameters are estimated using partially-independent component analysis, supported by a subset of differentially-expressed genes. We demonstrate the principle of the approach on the data sets derived from mixed cell lines of small round blue cell tumors. Because accurate source separation can be achieved blindly and numerically, we anticipate that computational correction of tissue heterogeneity will be useful in a wide variety of gene microarray studies.

Original languageEnglish (US)
Title of host publication2003 IEEE 13th Workshop on Neural Networks for Signal Processing, NNSP 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages23-32
Number of pages10
ISBN (Electronic)0780381777
DOIs
StatePublished - 2003
Externally publishedYes
Event13th IEEE Workshop on Neural Networks for Signal Processing, NNSP 2003 - Toulouse, France
Duration: Sep 17 2003Sep 19 2003

Publication series

NameNeural Networks for Signal Processing - Proceedings of the IEEE Workshop
Volume2003-January

Conference

Conference13th IEEE Workshop on Neural Networks for Signal Processing, NNSP 2003
Country/TerritoryFrance
CityToulouse
Period9/17/039/19/03

Bibliographical note

Publisher Copyright:
© 2003 IEEE.

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