pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes
暂无分享,去创建一个
Hsien-Da Huang | Wen-Ling Chan | Jan-Gowth Chang | Wen-Kuang Yang | Hsien-Da Huang | Jan-Gowth Chang | Wen-Ling Chan | Wen-Kuang Yang
[1] C. Burge,et al. Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.
[2] Oliver H. Tam,et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes , 2008, Nature.
[3] Stijn van Dongen,et al. miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..
[4] Ana Kozomara,et al. miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..
[5] Michael Zuker,et al. Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..
[6] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[7] Melissa D. Lehti-Shiu,et al. Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice1[C][W][OA] , 2009, Plant Physiology.
[8] Jan Krüger,et al. RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..
[9] M. Gerstein,et al. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes , 2009, Genome Biology.
[10] Li Lin,et al. Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. , 2011, Cancer cell.
[11] M. O'Shea,et al. Neuronal Expression of Neural Nitric Oxide Synthase (nNOS) Protein Is Suppressed by an Antisense RNA Transcribed from an NOS Pseudogene , 1999, The Journal of Neuroscience.
[12] Annie P. Chiang,et al. Genome‐wide identification of pseudogenes capable of disease‐causing gene conversion , 2006, Human mutation.
[13] Gene W. Yeo,et al. Divergent Transcription from Active Promoters , 2008, Science.
[14] Ron Edgar,et al. Gene Expression Omnibus ( GEO ) : Microarray data storage , submission , retrieval , and analysis , 2008 .
[15] Boris Lenhard,et al. RNAdb 2.0—an expanded database of mammalian non-coding RNAs , 2006, Nucleic Acids Res..
[16] M. Gerstein,et al. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability , 2005, Nucleic acids research.
[17] Anton J. Enright,et al. Human MicroRNA Targets , 2004, PLoS biology.
[18] N. Macmichael,et al. Notes , 1947, Edinburgh Medical Journal.
[19] N. Vinckenbosch,et al. Evolutionary fate of retroposed gene copies in the human genome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[20] Sean R. Eddy,et al. Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..
[21] A. Riggs,et al. Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[22] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[23] P. Harrison,et al. Assessing the genomic evidence for conserved transcribed pseudogenes under selection , 2009, BMC Genomics.
[24] D. Bartel,et al. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs , 2008, Nature.
[25] Y. Sakaki,et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes , 2008, Nature.
[26] Kanako O. Koyanagi,et al. Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones , 2004, PLoS Biology.
[27] C. Burge,et al. Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.
[28] Michael O'Shea,et al. Evolution of nitric oxide synthase regulatory genes by DNA inversion. , 2002, Molecular biology and evolution.
[29] Mouchiroud Dominique,et al. HOPPSIGEN: a database of human and mouse processed pseudogenes , 2004, Nucleic Acids Research.
[30] R. Nicholls,et al. The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans , 2006, Proceedings of the National Academy of Sciences.
[31] Shwu-Fan Ma,et al. A transcribed pseudogene of MYLK promotes cell proliferation , 2011, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[32] Hongmin Li,et al. A Precisely Regulated Gene Expression Cassette Potently Modulates Metastasis and Survival in Multiple Solid Cancers , 2008, PLoS genetics.
[33] Mauno Vihinen,et al. PseudoGeneQuest – Service for identification of different pseudogene types in the human genome , 2008, BMC Bioinformatics.
[34] Kiyoshi Asai,et al. The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs , 2008, Nucleic Acids Res..
[35] Zhan Yu,et al. Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures , 2007, BMC Genomics.
[36] Yi-Hsuan Chen,et al. miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes , 2007, Nucleic Acids Res..
[37] S. Batalov,et al. A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[38] Mark Gerstein,et al. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. , 2005, Journal of molecular biology.
[39] P. Pandolfi,et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.
[40] Adel Khelifi,et al. HOPPSIGEN: a database of human and mouse processed pseudogenes , 2005, Nucleic Acids Res..
[41] P. Hevezi,et al. Gene expression analyses reveal molecular relationships among 20 regions of the human CNS , 2006, Neurogenetics.
[42] Jian-Dong Huang,et al. Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli , 2005, Nucleic acids research.
[43] Gautier Koscielny,et al. Ensembl 2012 , 2011, Nucleic Acids Res..
[44] N. Perrimon,et al. An endogenous small interfering RNA pathway in Drosophila , 2008, Nature.
[45] John J. Rossi,et al. Strategies for silencing human disease using RNA interference , 2007, Nature Reviews Genetics.
[46] Tsippi Iny Stein,et al. In-silico human genomics with GeneCards , 2011, Human Genomics.
[47] A. Mighell,et al. Vertebrate pseudogenes , 2000, FEBS letters.
[48] Mark Gerstein,et al. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation , 2006, Nucleic Acids Res..
[49] Fred H. Gage,et al. Alternative Splicing Events Identified in Human Embryonic Stem Cells and Neural Progenitors , 2007, PLoS Comput. Biol..
[50] Ryan D. Morin,et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. , 2008, Genome research.
[51] Taishin Kin,et al. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells , 2008, Nature.
[52] Tao Liu,et al. NONCODE v2.0: decoding the non-coding , 2007, Nucleic Acids Res..
[53] Laurent Lestrade,et al. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs , 2005, Nucleic Acids Res..
[54] Atsushi Yoshiki,et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene , 2003, Nature.
[55] M. Kimmel,et al. Conflict of interest statement. None declared. , 2010 .
[56] Philipp Kapranov,et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. , 2007, Genome research.
[57] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[58] L. Lim,et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.
[59] Z. Weng,et al. Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells , 2008, Science.