title: Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma.
abstract: BACKGROUND
  Long non-coding RNAs (lncRNAs) are pervasively transcribed in the genome. They have important regulatory functions in chromatin remodeling and gene expression. Dysregulated lncRNAs have been studied in cancers, but their role in esophageal squamous cell carcinoma (ESCC) remains largely unknown. We have conducted lncRNA expression screening and a genome-wide analysis of lncRNA and coding gene expression on primary tumor and adjacent normal tissue from four ESCC patients, tend to understand the functionality of lncRNAs in carcinogenesis of esopheagus in combination with experimental and bioinformatics approach.
  
  
  METHODS
  LncRNA array was used for coding and non-coding RNA expression. R program and Bioconductor packages (limma and RedeR) were used for differential expression and co-expression network analysis, followed by independent confirmation and functional studies of inferred onco-lncRNA ESCCAL-1 using quantitative real time polymerase chain reaction, small interfering RNA-mediated knockdown, apoptosis and invasion assays in vitro.
  
  
  RESULTS
  The global coding and lncRNA gene expression pattern is able to distinguish ESCC from adjacent normal tissue. The co-expression network from differentially expressed coding and lncRNA genes in ESCC was constructed, and the lncRNA function may be inferred from the co-expression network. LncRNA ESCCAL-1 is such an example as a predicted novel onco-lncRNA, and it is overexpressed in 65% of an independent ESCC patient cohort (n = 26). More over, knockdown of ESCCAL-1 expression increases esophageal cancer cell apoptosis and reduces the invasion in vitro.
  
  
  CONCLUSIONS
  Our study uncovered the landscape of ESCC-associated lncRNAs. The systematic analysis of coding and lncRNAs co-expression network increases our understanding of lncRNAs in biological network. ESCCAL-1 is a novel putative onco-lncRNA in esophageal cancer development.
authors.affiliation: Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, Zhengzhou, 450007, PR, China. haoyibin0506@163.com.
authors.forename: Yibin
authors.initials: Y
authors.lastname: Hao
authors.affiliation: Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, Zhengzhou, 450007, PR, China. wuwei@ucalgary.ca.|Department of Pathology and Experimental Medicine, University of Calgary, Calgary, AB, Canada. wuwei@ucalgary.ca.
authors.forename: Wei
authors.initials: W
authors.lastname: Wu
authors.affiliation: Science and Education Department, Health Bureau of ZhengZhou, Zhengzhou, China. 3013406367@qq.com.
authors.forename: Fachun
authors.initials: F
authors.lastname: Shi
authors.affiliation: Department of Biochemistry, Bioscience Center and Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil. rodrigo.dalmolin@ufrgs.br.
authors.forename: Rodrigo J S
authors.initials: RJ
authors.lastname: Dalmolin
authors.affiliation: Medical School, Zhengzhou University, Zhengzhou, Henan, China. mingyan@zzu.edu.cn.
authors.forename: Ming
authors.initials: M
authors.lastname: Yan
authors.affiliation: Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, Zhengzhou, 450007, PR, China. 910100538@qq.com.
authors.forename: Fu
authors.initials: F
authors.lastname: Tian
authors.affiliation: Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, Zhengzhou, 450007, PR, China. 2290773710@qq.com.
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Chen
authors.affiliation: Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, Zhengzhou, 450007, PR, China. 13938238530@139.com.
authors.forename: Guoyong
authors.initials: G
authors.lastname: Chen
authors.affiliation: Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, Zhengzhou, 450007, PR, China. caoweiyu@hotmail.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Cao
mesh_terms: D000368:Aged; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis* / Q000235:genetics*; D004938:Esophageal Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D000077277:Esophageal Squamous Cell Carcinoma; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D008297:Male; D011237:Predictive Value of Tests; D062085:RNA, Long Noncoding / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding