The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

Keywords

Biology, Gene, Human genome, Genetics, RNA splicing

References

• Using geneid to Identify GenesEnrique Blanco, Genı́s Parra, Roderic Guigó — 2002
• RNA-Seq: a revolutionary tool for transcriptomicsZhong Wang, Mark Gerstein, M Snyder — 2009
• MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles.Hongjae Sunwoo, Marcel E. Dinger, Jeremy E. Wilusz — 2009
• Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammalsMitchell Guttman, Ido Amit, Manuel Garber — 2009
• The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to ChromatinTakashi Nagano, Jennifer A. Mitchell, Lionel A. Sanz — 2008
• 3’ end processing of a long nuclear-retained non-coding RNA yields a tRNA-like cytoplasmic RNAJeremy E. Wilusz, Susan M. Freier, David L. Spector — 2008
• High-resolution profiling of histone methylations in the human genome.Artem Barski, Suresh Cuddapah, Kairong Cui — 2007
• Differentiating Protein-Coding and Noncoding RNA: Challenges and AmbiguitiesMarcel E. Dinger, Ken C. Pang, Tim R. Mercer — 2008
• ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWASÉric Pasmant, Audrey Sabbagh, Michel Vidaud — 2011
• The Genetic Signatures of Noncoding RNAsJohn S. Mattick — 2009
• lncRNAs transactivate Staufen1-mediated mRNA decay by duplexing with 3'UTRs via Alu elementsChenguang Gong, Lynne E. Maquat — 2011
• The steroid receptor RNA activator is the first functional RNA encoding a proteinShilpa Chooniedass‐Kothari, Ethan Emberley, Mohammad K. Hamedani — 2004
• Most “Dark Matter” Transcripts Are Associated With Known GenesHarm van Bakel, Corey Nislow, Benjamin J. Blencowe — 2010
• Basic local alignment search tool.Stephen F. Altschul, Warren Gish, Webb Miller — 1990
• The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus.Neil Brockdorff, Alan Ashworth, Graham F. Kay — 1992
• The evolution of RNAs with multiple functions.Marcel E. Dinger, Dennis Gascoigne, John S. Mattick — 2011
• Transcriptome genetics using second generation sequencing in a Caucasian populationStephen B. Montgomery, Michael Sammeth, María Gutiérrez‐Arcelus — 2010
• A novel family of plasmid-transferred anti-sense ncRNAsSven Findeiß, Cornelius Schmidtke, Peter F. Stadler — 2010
• NRED: a database of long noncoding RNA expressionMarcel E. Dinger, Ken C. Pang, Tim R. Mercer — 2008
• Activation of p53 by MEG3 Non-coding RNA*Yunli Zhou, Ying Zhong, Yingying Wang — 2007

Cited by

• Methods for the Study of Long Noncoding RNA in Cancer Cell SignalingYi Feng, Zhongyi Hu, Youyou Zhang — 2014
• Potential Pathological and Functional Links Between Long Noncoding RNAs and HematopoiesisFelicity Heal — 2013
• Non-coding RNAs turn up the heat: An emerging layer of novel regulators in the mammalian heat shock responseRobert F. Place, Emily J. Noonan — 2013
• Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals徐树德 — 2014
• Tissue-specific RNA-Seq in Human Evoked Inflammation Identifies Blood and Adipose LincRNA Signatures of Cardio-metabolic DiseasesAnnie Pohlman — 2014
• Regulation of metabolism by long, non-coding RNAsAlberto T. Pérez — 2014
• Structured RNAs and synteny regions in the pig genomeLuis Llopis Portugal, María del Pilar Sainz de Baranda Andújar — 2014
• Single cell dissection of early kidney development: multilineage primingEric W. Brunskill, Joo‐Seop Park, Eunah Chung — 2014
• Length and GC Content Variability of Introns among Teleostean Genomes in the Light of the Metabolic Rate Hypothesis稔 山田, 廣 河村, 英夫 森高 — 2014
• Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implicationsSalus Herrero — 2014
• Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features.Joaquim de Montezuma de Carvalho — 2015
• Developmental regulation of human cortex transcription and its clinical relevance at base resolutionRafael Gil Reina — 2014
• Characterization of Novel Transcripts of Human Papillomavirus Type 16 Using Cap Analysis Gene Expression TechnologyAlec Bartsch, Karsten Specht — 2014
• Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencingSteven G. McCafferty — 2015
• The long non-coding RNA HNF1A-AS1 regulates proliferation and metastasis in lung adenocarcinomaMárcia Carréra Campos Leal, I Jiménez Pulido — 2015
• C-It-Loci: a knowledge database for tissue-enriched loci昝胜锋 — 2015
• Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq dataZheng Zhao, Jing Bai, Aiwei Wu — 2015
• Altered Long Noncoding RNA Expression Precedes the Course of Parkinson’s Disease—a Preliminary ReportGabriel Josipovici — 2016
• Epigenetic Regulation of Bone cellsKathryn C. Campbell, Stephen Hill, John Podd — 2016
• Long noncoding RNA LINP1 regulates double strand DNA break repair in triple negative breast cancerChon Tejedor — 2016

Related papers

• Molecular cloning and tissue distribution of a short form chicken leptin receptor mRNA.Xiaojun Liu, Ian Dunn, P. J. Sharp — 2007
• The ENCODE (ENCyclopedia Of DNA Elements) Project2004
• The ENCODE (ENCyclopedia Of DNA Elements) Project The ENCODE Project ConsortiumMark S. Guyer, S. Kamholz, Laura A. Liefer — 2004
• A decade of human genome project conclusion: Scientific diffusion about our genome knowledgeFernanda Moraes, Andréa Carla de Souza Góes — 2016
• Genomics: Encyclopedia of DNARichard Dahl — 2004
• A Brief Analysis of Encyclopedia of DNA ElementsMingyu Yang — 2013
• A User's Guide to the Encyclopedia of DNA Elements (ENCODE)The ENCODE Project Consortium — 2011
• A Brief Review on the Human Encyclopedia of DNA Elements (ENCODE) ProjectHongzhu Qu, Xiangdong Fang — 2013