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A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs

2019 Briefings in Bioinformatics  
We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome.  ...  Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs.  ...  Funding Federal Ministry of Education and Research (BMBF grant FKZ 031L0129B and Era-Net grant 01KT1801 to M.K. and T.D.); European Research Council (ERC) grant Longheart to T.T.  ... 
doi:10.1093/bib/bbz066 pmid:31578571 pmcid:PMC7373182 fatcat:slrhunxssfcujnlfgl7irbvwv4

zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs

Heena Dhiman, Shruti Kapoor, Ambily Sivadas, Sridhar Sivasubbu, Vinod Scaria, Ramani Ramchandran
2015 PLoS ONE  
Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases.  ...  We created a comprehensive resource which houses the annotation of lncRNAs as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion  ...  Authors acknowledge funding from the Council of Scientific and Industrial Research (CSIR) India zflncRNApedia: An Online Resource for Zebrafish Long Non-Coding RNAs  ... 
doi:10.1371/journal.pone.0129997 pmid:26065909 pmcid:PMC4466246 fatcat:voyth5dokfa4rnjyyfe3yrewrq

Paradigm shifts in genomics through the FANTOM projects

Michiel de Hoon, Jay W. Shin, Piero Carninci
2015 Mammalian Genome  
While the biological function has been elucidated for some lncRNAs, more than 98 % of them remain without a known function.  ...  The FANTOM Consortium has provided the most comprehensive mouse cDNA collection for functional studies and extensive maps of the human and mouse transcriptome comprising promoters, enhancers, as well as  ...  We are mainly supported by a Research Grant from Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT) to RIKEN Center for Life Science Technologies.  ... 
doi:10.1007/s00335-015-9593-8 pmid:26253466 pmcid:PMC4602071 fatcat:7y5if7dg7fao3pp6wogpducl2y

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging

Xinyue Lu, Qiuzhong Zhou, Jin Liu, Lei Sun
2021 STAR Protocols  
Here, we describe a protocol for the organism-wide analysis of murine lncRNAs during aging.  ...  For complete details on the use and execution of this protocol, please refer to Zhou et al. (2020).  ...  ACKNOWLEDGMENTS AUTHOR CONTRIBUTIONS L.S. and J.L. designed the study. X.L. and Q.Z. analyzed and interpreted the results. L.S., J.L., X.L., and Q.Z. drafted and edited the manuscript.  ... 
doi:10.1016/j.xpro.2021.100397 pmid:33786463 pmcid:PMC7994534 fatcat:y3kh5cu72rffti4ftlj2e2cvmm

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung Chau Hon, Michiel de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki, Piero Carninci, Takeya Kasukawa (+1 others)
2018 Nucleic Acids Research  
We have also expanded the CAGE analysis to cover rat, dog, chicken, and macaque species for a limited number of cell types.  ...  We have expanded the resource by employing different assays, such as RNA-seq, short RNA-seq and a paired-end protocol for CAGE (CAGEscan), to provide new angles to study the transcriptome.  ...  Forrest for scientific coordination of the FANTOM5 collaboration, Dr C. Plessy for helping the manuscript preparation, J. Harsh-  ... 
doi:10.1093/nar/gky1099 pmid:30407557 pmcid:PMC6323950 fatcat:xc6iffwzbngsdcqsrm7aptzgxa

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity [chapter]

Duy N. Do, Pier-Luc Dudemaine, Bridget Fomenky, Eveline M. Ibeagha-Awemu
2017 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health  
for a better understanding of the regulatory architecture of livestock phenotypes.  ...  Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identification of ncRNAs and functional inference of identified ncRNAs, with emphasis  ...  Acknowledgements We acknowledge financial support from Agriculture and Agri-Food Canada. Author details Duy N. Do 1,2 , Pier-Luc Dudemaine 1 , Bridget Fomenky 1,3 and Eveline M.  ... 
doi:10.5772/intechopen.69872 fatcat:qcwzw6aot5ew3bhosfqieumrge

A systematic review of computational methods for predicting long noncoding RNAs

Xinran Xu, Shuai Liu, Zhihao Yang, Xiaohan Zhao, Yaozhen Deng, Guangzhan Zhang, Jian Pang, Chengshuai Zhao, Wen Zhang
2021 Briefings in Functional Genomics  
Accurately and rapidly distinguishing long noncoding RNAs (lncRNAs) from transcripts is prerequisite for exploring their biological functions.  ...  Therefore, we develop a Python package ezLncPred, which provides a pragmatic command line implementation to utilize nine state-of-the-art lncRNA prediction methods.  ...  LncRNA prediction is the prerequisite for studying and understanding biogenesis and functions of lncRNAs.  ... 
doi:10.1093/bfgp/elab016 pmid:33754153 fatcat:zj5uppfkrjdczdtnnjuxemzcke

Identification of long non-coding RNAs in insects genomes

Fabrice Legeai, Thomas Derrien
2015 Current Opinion in Insect Science  
In this review, we first focus on what is known about experimentally validated lncRNAs in insects and then review bioinformatic methods to annotate lncRNAs in the genomes of hexapods.  ...  Among the many classes of non-coding RNAs (ncRNAs) identified the last decade, long non-coding RNAs (lncRNAs) represent a diverse and numerous repertoire of important ncRNAs, reinforcing the view that  ...  Acknowledgements The authors wish to thank Sue Brown and Denis Tagu for their comments and corrections on the manuscript.  ... 
doi:10.1016/j.cois.2015.01.003 pmid:32846672 fatcat:scmub7p2ozc4hlzmtf7cal7bmy

Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis

Adam W. Turner, Doris Wong, Mohammad Daud Khan, Caitlin N. Dreisbach, Meredith Palmore, Clint L. Miller
2019 Frontiers in Cardiovascular Medicine  
Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome.  ...  Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets  ...  LncADeep provides enriched pathways and functional modules for lncRNA functional annotation by integrating KEGG and Reactome Pathway databases in a deep learning framework (211) .  ... 
doi:10.3389/fcvm.2019.00009 pmid:30838214 pmcid:PMC6389617 fatcat:wgp4kijwafanrkzphz3htmhxga

Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis

Letizia Da Sacco, Antonella Baldassarre, Andrea Masotti
2011 International Journal of Molecular Sciences  
Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.  ...  LncRNAs are also implicated in a number of diseases.  ...  This integrated and comprehensive reference catalog could help to analyze the global properties of lncRNAs and facilitate further studies on functional classification of these non-coding genes.  ... 
doi:10.3390/ijms13010097 pmid:22312241 pmcid:PMC3269675 fatcat:t7vzf3w7l5apjoatnkhqhlwbge

Identification and integrated analysis of differentially expressed lncRNAs and circRNAs reveal the potential ceRNA networks during PDLSC osteogenic differentiation

Xiuge Gu, Mengying Li, Ye Jin, Dongxu Liu, Fulan Wei
2017 BMC Genetics  
Conclusions: This study comprehensively identified lncRNAs/circRNAs and first integrated their potential ceRNA function during PDLSC osteogenic differentiation.  ...  However, comprehensive identification and integrated analysis of lncRNAs and circRNAs acting as ceRNAs during PDLSC osteogenic differentiation have not been performed.  ...  Acknowledgments We acknowledge the anonymous reviewers and academic editors for their constructive suggestions on the previous version of the manuscript.  ... 
doi:10.1186/s12863-017-0569-4 pmid:29197342 pmcid:PMC5712120 fatcat:fo3yzpp5ubgd7nwoxif5ymxj7y

Profiling of RNAs from Human Islet-Derived Exosomes in a Model of Type 1 Diabetes

Preethi Krishnan, Farooq Syed, Nicole Jiyun Kang, Raghavendra G. Mirmira, Carmella Evans-Molina
2019 International Journal of Molecular Sciences  
Taken together, our data identify RNAs that are dysregulated under cytokine stress in human islet-derived exosomes, providing a comprehensive catalog of protein coding and noncoding RNAs that may serve  ...  RNAs with a fold change ≥1.3 and a p-value <0.05 were considered as differentially expressed. mRNAs and miRNAs represented the most abundant long and small RNA species, respectively.  ...  Since there are no known predictive tools for the functional enrichment analysis of lncRNAs, one way to understand the function of lncRNAs is to identify the protein coding genes that correlate with the  ... 
doi:10.3390/ijms20235903 pmid:31775218 pmcid:PMC6928620 fatcat:z4y5umihlvafpdudwibqbhe2zq

The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource

Feng Hong, Si-Hua Mo, Xing-Yu Lin, Jinzhi Niu, Jian Yin, Dong Wei
2020 Frontiers in Genetics  
Very few functional studies have so far focused on the developmental and reproductive biology at a molecular level, because of the lack of comprehensive genetic information.  ...  A total of 46.8 Gb nucleotides and 15,938 non-redundant full-length transcripts were obtained, 13,498 (84.69%) of which were annotated into seven databases.  ...  This full-length transcriptome contributes to the first comprehensive dataset of genetic information for this species, including protein-coding genes, lncRNAs, and microsatellites.  ... 
doi:10.3389/fgene.2020.558394 pmid:33304379 pmcid:PMC7693467 fatcat:lmxq3ivxlza7xbkmqwwthalkem

Exploring Additional Valuable Information From Single-Cell RNA-Seq Data

Yunjin Li, Qiyue Xu, Duojiao Wu, Geng Chen
2020 Frontiers in Cell and Developmental Biology  
Additionally, we survey the integration of single-cell and bulk RNA-seq datasets for deconvoluting the cell composition of large-scale bulk samples and linking single-cell signatures to patient outcomes  ...  Most of the scRNA-seq studies mainly focused on the dissection of cell types/states, developmental trajectory, gene regulatory network, and alternative splicing.  ...  For example, Yan et al. (2013) integrated genomeindependent and genome-guided assembly methods to predict the new transcripts and detected a set of novel long noncoding RNAs (lncRNAs) that are functionally  ... 
doi:10.3389/fcell.2020.593007 pmid:33335900 pmcid:PMC7736616 fatcat:wbboyh6gjjbvxbutsmtmv53ztq

The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer

Naiade Calanca, Cecilie Abildgaard, Cláudia Aparecida Rainho, Silvia Regina Rogatto
2020 Cancers  
Comprehensive large-scale sequencing and bioinformatics analyses have uncovered a myriad of cancer-associated long noncoding RNAs (lncRNAs).  ...  The resources and mechanisms presented herein can improve the understanding of OC biology and provide the basis for further investigations regarding the selection of novel biomarkers and therapeutic targets  ...  Collects a comprehensive set of human lncRNAs and provides LncBook multi-omics data integration, functional http: // [108,113] annotation, and disease association for these transcripts  ... 
doi:10.3390/cancers12092701 pmid:32967233 pmcid:PMC7563210 fatcat:so7rj7275vb6fnlihwiejog6qq
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