title: Identification of key genes involved in HER2-positive breast cancer.
abstract: OBJECTIVE
  As an invasive cancer, breast cancer is the most common tumour in women and is with high mortality. To study the mechanisms of HER2-positive breast cancer, we analyzed microarray of GSE52194.
  
  
  METHODS
  GSE52194 was downloaded from Gene Expression Omnibus including 5 HER2-positive breast cancer samples and 3 normal breast samples. Using cuffdiff software, differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DE-lncRNAs) were screened. Functions of the DEGs were analyzed by Gene Ontology (GO) and pathway enrichment analyses. Then, protein-protein interaction (PPI) network of the DEGs was constructed using Cytoscape and modules of the PPI network were screened by CFinder. Moreover, lncRNA-DEG pairs were screened.
  
  
  RESULTS
  Total 209 lncRNA transcriptions were predicted, and 996 differentially expressed transcriptions were screened. Besides, FOS had interaction relationships with EGR1 and SOD2 separately in module E and F of the PPI network for the DEGs. Moreover, there were many lncRNA-DEG pairs (e.g. TCONS_00003876-EGR1, TCONS_00003876-FOS, lnc-HOXC4-3:1-FOS, lnc-HOXC4-3:1-BCL6B, lnc-TEAD4-1:1-FOS and lnc-TEAD4-1:1-BCL6B), meanwhile, co-expressed DEGs of TCONS_00003876, lnc-HOXC4-3:1 and lnc-TEAD4-1:1 were enriched in p53 signaling pathway, MAPK signaling pathway and cancer-related pathways, respectively.
  
  
  CONCLUSIONS
  ANXA1, EGR1, BCL6, SOD2, FOS, TCONS_00003876, lnc-HOXC4-3:1 and lnc-TEAD4-1:1 might play a role in HER2-positive breast cancer.
authors.affiliation: Department of Pathology, Second People's Hospital of Guangdong Province/Guangdong Provincial Emergency Hospital, Guangzhou, P.R. China. kejingwangkjw@163.com.
authors.forename: B-L
authors.initials: BL
authors.lastname: Zhong
authors.forename: L-J
authors.initials: LJ
authors.lastname: Bian
authors.forename: G-M
authors.initials: GM
authors.lastname: Wang
authors.forename: Y-F
authors.initials: YF
authors.lastname: Zhou
authors.forename: Y-Y
authors.initials: YY
authors.lastname: Chen
authors.forename: F
authors.initials: F
authors.lastname: Peng
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D062085:RNA, Long Noncoding / Q000235:genetics; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D062085:RNA, Long Noncoding; D018719:Erb-b2 Receptor Tyrosine Kinases; C508053:ERBB2 protein, human