Affiliations: [a] Department of Science and Education, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China | [b] Pharmacy Intravenous Admixture Service, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China | [c] Department of Neurosurgery, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China | [d] Department of Cardiology, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China | [e] Department of General Surgery, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China
Correspondence:
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Corresponding author: Lei Wang, Department of Science and Education,, The People's Hospital of Zhangqiu, NO 1920. Huiquan Road, Zhangqiu 250200, Shandong, China. Tel.: +86 0531 83251203; Fax: +86 0531 83250517; E-mail:wanglei10059@sina.com
Abstract: OBJECTIVE: To investigate novel gene sets related to breast cancer
(BC) using differential co-expression and differential expression (DECODE). METHODS: T statistics was used to quantify the degree of DE of each
gene, and then Z was adopted to quantify the correlation difference between
expression levels of two genes. Two optimal thresholds for defining
substantial change in DE and DC were selected for each gene using chi-square
maximization, and the corresponding gene was defined as the optimal gene.
Based on the optimal thresholds, genes were categorized into four partitions
with either high or low DC and DE characteristics. Finally, we evaluated the
functional relevance of a gene partition with high DE and high DC, and the
gene set with best association was considered as the optimal functional gene
set. RESULTS: The optimal thresholds for DC and DE were respective 2.254
and 1.616, and the optimal gene was UBE2Q2L. Based on the optimal
thresholds, genes were divided into four partitions including HDE-HDC (875
genes), HED-LDC (8038 genes), LDE-HDC (678 genes), and LDE-LDC (10516
genes). The best associated gene set was ``fatty acid catabolic process''
with 34 HDC and HDE partitions. Among these partitions, UBE2Q2L attained the
highest minimum FI gain of 18.973. CONCLUSION: UBE2Q2L and fatty acid catabolic process might be
potentially useful signatures in diagnostic purposes for BC.
Keywords: Breast cancer, differential co-expression and differential expression, functional information
