title: A new RNA-seq method to detect the transcription and non-coding RNA in prostate cancer.
abstract: Prostate cancer is a big killer in many regions especially American men, and this year, the diagnosed rate rises rapidly. We aimed to find the biomarker or any changing in prostate cancer patients. With the development of next generation sequencing, much genomic alteration has been found. Here, basing on the RNA-seq result of human prostate cancer tissue, we tried to find the transcription or non-coding RNA expressed differentially between normal tissue and prostate cancer tissue. 10 T sample data is the RNA-seq data for prostate cancer tissue in this study, we found the differential gene is TFF3-Trefoil factor 3, which was more than seven fold change from prostate cancer tissue to normal tissue, and the most outstanding transcript is C15orf21. Additionally, 9 lncRNAs were found according our method. Finally, we found the many important non-coding RNA related to prostate cancer, some of them were long non-coding RNA (lncRNA).
authors.affiliation: Department of Urology, Qianfoshan Hospital Affiliated to Shandong University, No.16766 Jingshi Road, Jinan, Shandong Province, 250014, China.
authors.forename: Xiao-Ming
authors.initials: XM
authors.lastname: Zhang
authors.forename: Zhong-Wei
authors.initials: ZW
authors.lastname: Ma
authors.forename: Qiang
authors.initials: Q
authors.lastname: Wang
authors.forename: Jian-Ning
authors.initials: JN
authors.lastname: Wang
authors.forename: Ji-Wei
authors.initials: JW
authors.lastname: Yang
authors.forename: Xian-Duo
authors.initials: XD
authors.lastname: Li
authors.forename: Hao
authors.initials: H
authors.lastname: Li
authors.forename: Tong-Yi
authors.initials: TY
authors.lastname: Men
mesh_terms: D006801:Humans; D008297:Male; D010455:Peptides / Q000235:genetics; D011471:Prostatic Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic; D000071165:Trefoil Factor-3
chemical_list: D010455:Peptides; D062085:RNA, Long Noncoding; C082495:TFF3 protein, human; D000071165:Trefoil Factor-3
references.citation: Genes Dev. 2011 Sep 15;25(18):1915-27
references.pmid: 21890647
references.citation: Bioinformatics. 2009 Apr 15;25(8):1026-32
references.pmid: 19244387
references.citation: Genome Res. 2011 Jan;21(1):56-67
references.pmid: 21036922
references.citation: Nat Protoc. 2012 Mar 01;7(3):562-78
references.pmid: 22383036
references.citation: Nat Rev Mol Cell Biol. 2008 Mar;9(3):219-30
references.pmid: 18270516
references.citation: Nature. 2009 Mar 5;458(7234):97-101
references.pmid: 19136943
references.citation: Prostate. 2004 Nov 1;61(3):209-14
references.pmid: 15368472
references.citation: Nature. 2007 Aug 2;448(7153):595-9
references.pmid: 17671502
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31
references.pmid: 20972220
references.citation: EMBO Rep. 2001 Nov;2(11):986-91
references.pmid: 11713189
references.citation: BMC Urol. 2004 Dec 10;4(1):14
references.pmid: 15588310
references.citation: Nat Genet. 2012 May 20;44(6):685-9
references.pmid: 22610119
references.citation: Cell Res. 2012 May;22(5):786-8
references.pmid: 22453238
references.citation: Biotechniques. 2008 Jul;45(1):81-94
references.pmid: 18611170
references.citation: Nat Rev Genet. 2009 Mar;10(3):155-9
references.pmid: 19188922
references.citation: Cancer Res. 2008 Feb 1;68(3):645-9
references.pmid: 18245462
references.citation: Clin Cancer Res. 2006 Feb 1;12(3 Pt 1):807-12
references.pmid: 16467092
references.citation: Nature. 2010 Apr 15;464(7291):1071-6
references.pmid: 20393566
references.citation: Nature. 2012 Jul 12;487(7406):239-43
references.pmid: 22722839
references.citation: Cell Res. 2012 May;22(5):806-21
references.pmid: 22349460
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: Nature. 2011 Feb 10;470(7333):214-20
references.pmid: 21307934
references.citation: Genome Res. 2011 Jun;21(6):991-8
references.pmid: 21536721