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NONCODEv4: exploring the world of long non-coding RNA genes

Chaoyong Xie, Jiao Yuan, Hui Li, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, Runsheng Chen, Yi Zhao
2013 Nucleic Acids Research  
Particularly, the number of long non-coding RNA (lncRNA) has increased sharply from 73 327 to 210 831.  ...  Additionally, we present expression profile of lncRNA genes by graphs based on public RNA-seq data for human and mouse, as well as predict functions of these lncRNA genes.  ...  Xiaohua Shen of Tsinghua University for help during the course of this work. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1222 pmid:24285305 pmcid:PMC3965073 fatcat:hh44zvq4urefxi43d7xa7c3pv4

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

Wen Chen, Xuan Zhang, Jing Li, Shulan Huang, Shuanglin Xiang, Xiang Hu, Changning Liu
2018 BMC Genomics  
Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized.  ...  Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA.  ...  Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s12864-018-4458-7 pmid:29764394 pmcid:PMC5954278 fatcat:j5adl6a35jh6zjqho72ggfj42a

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

Sandeep Chakraborty, Monica Britton, Jill Wegrzyn, Timothy Butterfield, Basuthkar J. Rao, Charles A. Leslie, Mallikarjuna Aradhaya, David Neale, Keith Woeste, Abhaya M. Dandekar
2015 F1000Research  
Xie C, Yuan J, Li H, et al.: NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 2014; 42(Database issue): D98-D103.  ...  Arrial RT, Togawa RC, Brigido Mde M: Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus paracoccidioides brasiliensis.  ...  Acknowledgements We are grateful to Mary Lou Mendum for her inputs in preparing the manuscript.  ... 
doi:10.12688/f1000research.6617.1 pmid:26870317 pmcid:PMC4732554 fatcat:qbh5yu5edjeo3fhbq55rsxqixe

Altered Expression of Long Noncoding RNAs in Blood After Ischemic Stroke and Proximity to Putative Stroke Risk Loci

Cheryl Dykstra-Aiello, Glen C. Jickling, Bradley P. Ander, Natasha Shroff, Xinhua Zhan, DaZhi Liu, Heather Hull, Miles Orantia, Boryana S. Stamova, Frank R. Sharp
2016 Stroke  
Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009;23:1494-1504. doi: 10.1101/gad.1800909. 21. Pink RC, Carter DR. Pseudogenes as regulators of biological function.  ...  Non-coding RNAs in human disease. Nat Rev Genet.2011;12:861-874. doi: 10.1038/nrg3074. 17. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Non-coding RNAs: regulators of disease.  ... 
doi:10.1161/strokeaha.116.013869 pmid:27834745 pmcid:PMC5127755 fatcat:iesjamwmvnflldgzyqrya6p6qu