title: Transcriptome profiling of prostate tumor and matched normal samples by RNA-Seq.
abstract: BACKGROUND
  RNA-Sequencing (RNA-Seq) has greatly influenced cancer researches, and it provides an unprecedented resolution in estimating gene expression and has less signal noises compared to cDNA microarray.
  
  
  OBJECTIVE
  We aimed to identify a list of protein-coding genes and lincRNAs that are expressed differentially between tumor and normal tissues.
  
  
  METHODS
  In this study, we analyzed including 10 human prostate tumor tissues and their matched normal tissues transcriptome dataset generated by recently developed RNA-Seq technology.
  
  
  RESULTS
  By aligning short reads to human RefSeq genes and lincRNAs, we identified 10 RefSeq genes that were differentially expressed between tumor and normal samples with a p-value < 0.05, which were sufficiently enough to distinguish these two groups. Further loosing the p-value cutoff to 0.1 identified an lincRNA which is antisense to Cullin-associated and neddulation-dissociated 1 (CAND1), whose expression is repressed in prostate tumor cells. By examining the expression of CAND1 and its antisense lincRNA in the transcriptome dataset, we found an interaction between them as high expression of CAND1 and low expression of lincRNA is normal samples, and verse visa in tumor samples.
  
  
  CONCLUSIONS
  These findings suggest the important usage of RNA-Seq in cancer studies for biomarker development and functional investigation.
authors.affiliation: Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China. jacky_zw2002@hotmail.com.
authors.forename: W
authors.initials: W
authors.lastname: Zhai
authors.forename: X-d
authors.initials: XD
authors.lastname: Yao
authors.forename: Y-f
authors.initials: YF
authors.lastname: Xu
authors.forename: B
authors.initials: B
authors.lastname: Peng
authors.forename: H-m
authors.initials: HM
authors.lastname: Zhang
authors.forename: M
authors.initials: M
authors.lastname: Liu
authors.forename: J-h
authors.initials: JH
authors.lastname: Huang
authors.forename: G-c
authors.initials: GC
authors.lastname: Wang
authors.forename: J-h
authors.initials: JH
authors.lastname: Zheng
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D016022:Case-Control Studies; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008297:Male; D011471:Prostatic Neoplasms / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D012334:RNA, Neoplasm / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; C486317:CAND1 protein, human; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D014157:Transcription Factors