title: Analyzing the differentially expressed genes and pathway cross-talk in aggressive breast cancer.
abstract: OBJECTIVE
  The aim of this study was to explore the genes and pathways involved in the aggressive breast cancer cells.
  
  
  METHODS
  The gene expression profiles of GSE40057, including four aggressive breast cell lines and six less aggressive cell lines, were downloaded from the Gene Expression Omnibus (GEO) database. The gene differential expression analysis was carried out with limma software with the method of Bayes for multiple tests. The gene ontology (GO) term enrichment and pathway cross-talk analysis were performed with the online tool of DAVID and Cytoscape software.
  
  
  RESULTS
  A total of 401 differentially expressed genes (DEG), such as pentraxin 3 (PTX3), snail family zinc finger 2 (SNAI2), interleukin-8/6 (IL-8/6), osteonectin (SPARC), matrix metallopeptidase-1 (MMP-1) and Ras-related protein Rab-25 (Rab 25), were identified between aggressive and less aggressive cell lines. They were mainly enriched in the GO terms of response to wounding, negative regulation of cell proliferation and calcium binding. Pathways in cancer dysfunctionally interacted with glyoxylate and dicarboxylate metabolism (P < 0.0001), basal transcription factors (P < 0.0001), tyrosine metabolism (P < 0.0001), calcium signaling pathway (P = 0.0021), FcγR-mediated phagocytosis (P = 0.0022), metabolism of xenobiotics by cytochrome P450 (P = 0.0097) and phagosome (P = 0.0102).
  
  
  CONCLUSIONS
  The screened aggressive cancer-associated DEG (PTX3, SNAI2, IL-8/6, SPARC, MMP-1 and Rab25) and significant pathways (calcium signaling pathway, tyrosine metabolism, alanine, aspartate and glutamate metabolism) give us new insights into the mechanism of aggressive breast cancer cells, and these DEG may become promising target genes in the treatment of metastatic breast cancer.
authors.affiliation: Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China.
authors.forename: Wen-Yan
authors.initials: WY
authors.lastname: Chen
authors.forename: Fang
authors.initials: F
authors.lastname: Wu
authors.forename: Zhen-Yu
authors.initials: ZY
authors.lastname: You
authors.forename: Zhan-Min
authors.initials: ZM
authors.lastname: Zhang
authors.forename: Yu-Ling
authors.initials: YL
authors.lastname: Guo
authors.forename: Lu-Xing
authors.initials: LX
authors.lastname: Zhong
mesh_terms: D001943:Breast Neoplasms / Q000378:metabolism*; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D063990:Gene Ontology; D006801:Humans; D020239:Receptor Cross-Talk
keywords: aggressive breast cancer; function enrichment analysis; pathway cross-talk analysis