Oncotarget

Research Papers:

Discovery and validation of a glioblastoma co-expressed gene module

Leland J. Dunwoodie, William L. Poehlman, Stephen P. Ficklin and Frank Alexander Feltus _

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Oncotarget. 2018; 9:10995-11008. https://doi.org/10.18632/oncotarget.24228

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Abstract

Leland J. Dunwoodie1, William L. Poehlman1, Stephen P. Ficklin2 and Frank Alexander Feltus1

1Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA

2Department of Horticulture, Washington State University, Pullman, WA 99164, USA

Correspondence to:

Frank Alexander Feltus, email: ffeltus@clemson.edu

Keywords: glioblastoma; systems biology; gene co-expression networks; complement system; cancer

Received: July 28, 2017     Accepted: January 09, 2018     Published: January 13, 2018

ABSTRACT

Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors. Among the proneural, neural, mesenchymal, and classical glioblastoma subtypes, these genes are most-highly expressed in the mesenchymal subtype. Furthermore, high expression of these genes is associated with decreased survival across each glioblastoma subtype. These genes are of interest to glioblastoma biology and our gene interaction discovery and validation workflow can be used to discover and validate co-expressed gene modules derived from any co-expression network.


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