title: Screening for the optimal gene and functional gene sets related to breast cancer using differential co-expression and differential expression analysis.
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.
  
  
  CONCLUSIONS
  UBE2Q2L and fatty acid catabolic process might be potentially useful signatures in diagnostic purposes for BC.
authors: Department of Science and Education, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China.
authors: Lei
authors: L
authors: Wang
authors: Pharmacy Intravenous Admixture Service, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China.
authors: Hong
authors: H
authors: Ma
authors: Department of Neurosurgery, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China.
authors: Lixia
authors: L
authors: Zhu
authors: Department of Science and Education, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China.
authors: Liping
authors: L
authors: Ma
authors: Department of Cardiology, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China.
authors: Lanting
authors: L
authors: Cao
authors: Department of General Surgery, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China.
authors: Hui
authors: H
authors: Wei
authors: Department of General Surgery, The People's Hospital of Zhangqiu, Zhangqiu, Shandong, China.
authors: Jumei
authors: J
authors: Xu
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D016022:Case-Control Studies; D055088:Early Detection of Cancer / Q000379:methods; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods
keywords: Breast cancer; differential co-expression and differential expression; functional information