ArticleCancer biomarkers : section A of Disease markers2016
Screening for the optimal gene and functional gene sets related to breast cancer using differential co-expression and differential expression analysis.
Article in Cancer biomarkers : section A of Disease markers, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
objectiveTo investigate novel gene sets related to breast cancer (BC) using differential co-expression and differential expression (DECODE).
methodsT 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.
resultsThe 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.
conclusionUBE2Q2L and fatty acid catabolic process might be potentially useful signatures in diagnostic purposes for BC.
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