title: pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.
abstract: RNA interference (RNAi) is a gene silencing process within living cells, which is controlled by the RNA-induced silencing complex with a sequence-specific manner. In flies and mice, the pseudogene transcripts can be processed into short interfering RNAs (siRNAs) that regulate protein-coding genes through the RNAi pathway. Following these findings, we construct an innovative and comprehensive database to elucidate siRNA-mediated mechanism in human transcribed pseudogenes (TPGs). To investigate TPG producing siRNAs that regulate protein-coding genes, we mapped the TPGs to small RNAs (sRNAs) that were supported by publicly deep sequencing data from various sRNA libraries and constructed the TPG-derived siRNA-target interactions. In addition, we also presented that TPGs can act as a target for miRNAs that actually regulate the parental gene. To enable the systematic compilation and updating of these results and additional information, we have developed a database, pseudoMap, capturing various types of information, including sequence data, TPG and cognate annotation, deep sequencing data, RNA-folding structure, gene expression profiles, miRNA annotation and target prediction. As our knowledge, pseudoMap is the first database to demonstrate two mechanisms of human TPGs: encoding siRNAs and decoying miRNAs that target the parental gene. pseudoMap is freely accessible at http://pseudomap.mbc.nctu.edu.tw/. Database URL: http://pseudomap.mbc.nctu.edu.tw/
authors: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan.
authors: Wen-Ling
authors: WL
authors: Chan
authors: Wen-Kuang
authors: WK
authors: Yang
authors: Hsien-Da
authors: HD
authors: Huang
authors: Jan-Gowth
authors: JG
authors: Chang
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D011544:Pseudogenes / Q000235:genetics*; D034741:RNA, Small Interfering / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering
references: Proc Natl Acad Sci U S A. 1986 Feb;83(3):679-83
references: 2418440
references: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12039-44
references: 16882727
references: FEBS Lett. 2000 Feb 25;468(2-3):109-14
references: 10692568
references: BMC Bioinformatics. 2008 Jul 02;9:299
references: 18597685
references: J Neurosci. 1999 Sep 15;19(18):7711-20
references: 10479675
references: PLoS Genet. 2008 Jul 18;4(7):e1000129
references: 18636107
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
references: 17991681
references: Science. 2005 Sep 2;309(5740):1559-63
references: 16141072
references: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references: 12824337
references: Nature. 2008 May 22;453(7194):534-8
references: 18404147
references: Nature. 2008 Jun 5;453(7196):793-7
references: 18463636
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W451-4
references: 16845047
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D59-66
references: 15608268
references: PLoS Biol. 2004 Jun;2(6):e162
references: 15103394
references: Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3220-5
references: 16492757
references: J Mol Biol. 2005 May 27;349(1):27-45
references: 15876366
references: Genome Res. 2009 Jan;19(1):92-105
references: 18955434
references: PLoS Biol. 2004 Nov;2(11):e363
references: 15502875
references: Mol Cell. 2007 Jul 6;27(1):91-105
references: 17612493
references: Nature. 2010 Jun 24;465(7301):1033-8
references: 20577206
references: BMC Genomics. 2009 Sep 15;10:435
references: 19754956
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D158-62
references: 16381836
references: Plant Physiol. 2009 Sep;151(1):3-15
references: 19641029
references: BMC Genomics. 2007 Oct 15;8:371
references: 17937804
references: Hum Genomics. 2011 Oct;5(6):709-17
references: 22155609
references: Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7
references: 15075390
references: Hum Mutat. 2006 Jun;27(6):545-52
references: 16671097
references: Genome Res. 2008 Apr;18(4):610-21
references: 18285502
references: Methods Enzymol. 2006;411:352-69
references: 16939800
references: Cancer Cell. 2011 Feb 15;19(2):232-43
references: 21316602
references: PLoS Comput Biol. 2007 Oct;3(10):1951-67
references: 17967047
references: Genome Res. 2003 Dec;13(12):2559-67
references: 14656963
references: Nat Rev Genet. 2007 Mar;8(3):173-84
references: 17304245
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D89-92
references: 18948287
references: Nature. 2003 May 1;423(6935):91-6
references: 12721631
references: Science. 2008 May 23;320(5879):1077-81
references: 18403677
references: Genome Res. 2002 Jun;12(6):996-1006
references: 12045153
references: Neurogenetics. 2006 May;7(2):67-80
references: 16572319
references: Cell. 2005 Jan 14;120(1):15-20
references: 15652477
references: Nucleic Acids Res. 2005 Apr 28;33(8):2374-83
references: 15860774
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D165-9
references: 18029362
references: Nature. 2008 Jun 5;453(7196):798-802
references: 18463631
references: FASEB J. 2011 Jul;25(7):2305-12
references: 21441351
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D55-60
references: 17099229
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90
references: 22086963
references: Science. 2008 Dec 19;322(5909):1849-51
references: 19056940
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D178-82
references: 17145715
references: Nature. 2008 May 22;453(7194):539-43
references: 18404146
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4
references: 15608160
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
references: 21037258
references: Genome Biol. 2009;10(1):R2
references: 19123937
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Nature. 2008 Jun 5;453(7196):803-6
references: 18463630
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D170-2
references: 18000000
references: Genome Res. 2007 Jun;17(6):839-51
references: 17568002
references: Mol Biol Evol. 2002 Aug;19(8):1228-33
references: 12140234