Long non‐coding RNAs (lncRNAs) refer to a class of non‐protein coding RNAs that are more than 0 nucleotides and are differentially accumulated in the nucleus and cytoplasm9 LncRNAs play various regulatory roles in the cell including regulation of development, stem cell pluripotency, cell growth and apoptosis and are frequentlyNONCODEv5, the systematic public database that is dedicated to the collection and annotation of lncRNA, has recorded 548,640 lncRNA transcripts from 17 different species, with the expression profiles of entire human and mouse genome being annotated 6To establish a highquality database of ncRNAs, all the articles related to drug resistance and ncRNAs were manually extracted from publications (Fig 1) (i) We searched all published studies in the PubMed database using the following combination of keywords "long noncoding RNA or lncRNA and drug and cancer," "microRNA or miRNA and drug and cancer," "circRNA and drug and cancer
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Noncodev5 a comprehensive annotation database for long non-coding rnas
Noncodev5 a comprehensive annotation database for long non-coding rnas-A comprehensive collection of 270,044 human lncRNAs and systematic curation of lncRNAs' annotation by multiomics data integration, function annotation and disease association MONOCLdb The MOuse NOnCode Lung database provides the annotations and expression profiles of mouse long noncoding RNAs (lncRNAs) involved in influenza and SARSCoV(iii) the RNA secondary structures of
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NONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res 46, D308–D314 doi /nar/gkx1107 PubMed Abstract CrossRef Full Text Google ScholarIntroduction Long noncoding RNAs (lncRNAs) are a recently discovered class of non protein coding transcripts encoded by many metazoan genomes Members of this class have been largely annotated in the recent years following the transcriptome annotation of metazoans using deep sequencing approaches 2–5By definition, lncRNAs are transcripts with a length of more than 0 nucleotides andGTF Long noncoding RNA gene annotation CHR It contains the comprehensive gene annotation of lncRNA genes on the reference
NONCODEV5 – a comprehensive annotation database for long noncoding RNAs November 17, 17 Leave a comment 4,627 Views NONCODE is a systematic database that is dedicated to presenting the most complete collection and annotation of noncoding RNAs (ncRNAs), especially long noncoding RNAs (lncRNAs)Skeletal muscle long noncoding RNAs (lncRNAs) were reported to be involved in the development of type 2 diabetes (T2D) However, little is known about the mechanism of skeletal muscle lncRNAs on hyperglycemia of diabetic GotoKakizaki (GK) rats at the age of 3 and 4 weeks To elucidate this, we used RNAsequencing to profile the skeletal muscle transcriptomes including lncRNAs and mRNAs, inNONCODEV5 – a comprehensive annotation database for long noncoding RNAs November 17, 17 Leave a comment 4,464 Views NONCODE is a systematic database that is dedicated to presenting the most complete collection and annotation of noncoding RNAs (ncRNAs), especially long noncoding RNAs (lncRNAs)
57 Fang S, Zhang L, Guo J, et al NONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res 18;46D308D314 58 Consortium TEP An integrated encyclopediaNONCODEV5 – a comprehensive annotation database for long noncoding RNAs NONCODE is a systematic database that is dedicated to presenting the most complete collection and annotation of noncoding RNAs (ncRNAs), especially long noncoding RNAs (lncRNAs)NONCODE is a comprehensive database that aims to present the most complete collection and annotation of noncoding RNAs, especially long noncoding RNAs (lncRNA genes), and thus NONCODE is essential to modern biological and medical research Scientists are producing a flood of new data from which ne
Invited Review Long Non Coding Rnas Important Regulators In The Development Function And Disorders Of The Central Nervous System Cuevas Diaz Duran 19 Neuropathology And Applied Neurobiology Wiley Online Library
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Lianhe Zhao's 8 research works with 167 citations and 3 reads, including HERB a highthroughput experiment and referenceguided database of traditional Chinese medicineThe number of lncRNAs in NONCODEv5 increased from 527 336 to 548 640 NONCODEv5 also introduced three important new features (i) human lncRNAdisease relationships and single nucleotide polymorphismlncRNAdisease relationships were constructed;Data LNCipedia is a public database for long noncoding RNA (lncRNA) sequence and annotation The current release contains 127,802 transcripts and 56,946 genes
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, 17 NONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res 46 D308 – D314 doi /nar/gkx1107 OpenUrl CrossRefData LNCipedia is a public database for long noncoding RNA (lncRNA) sequence and annotation The current release contains 127,802 transcripts and 56,946 genesNutrient stress is the most important environmental stress that limits plant growth and development Although recent evidence highlights the vital functions of long noncoding RNAs (lncRNA) in response to single nutrient stress in some model plants, a comprehensive investigation of the effect of lncRNAs in response to nutrient stress has not been performed in Arabidopsis thaliana
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NONCODEV5 a comprehensive annotation database for long noncoding RNAs Fang S,Zhang L,Guo J,Niu Y,Wu Y,Li H,Zhao L,Li X,Teng X,Sun X,Sun L,Zhang MQ,Chen R,Zhao Y Nucleic Acids Res 17 View Paper (PubMed) View PublicationNONCODEV5 – a comprehensive annotation database for long noncoding RNAs November 17, 17 Leave a comment 4,507 Views NONCODE is a systematic database that is dedicated to presenting the most complete collection and annotation of noncoding RNAs (ncRNAs), especially long noncoding RNAs (lncRNAs)Comprehensive gene annotation ALL It contains the comprehensive gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes) This is a superset of the main annotation file;
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NONCODEV5 a comprehensive annotation database for long noncoding RNAs Fang S,Zhang L,Guo J,Niu Y,Wu Y,Li H,Zhao L,Li X,Teng X,Sun X,Sun L,Zhang MQ,Chen R,Zhao Y Nucleic Acids Res 17 View Paper (PubMed) View PublicationWe describe an updated comprehensive database, LincSNP 30 Emerging evidences have shown the importance of long noncoding RNAs (lncRNAs) as novel regulators of many physical or pathological processes NONCODEV5 a comprehensive annotation database for long noncoding RNAsLong noncoding RNAs (lncRNAs) play important roles in cancerThey are involved in chromatin remodeling, as well as transcriptional and posttranscriptional regulation, through a variety of chromatinbased mechanisms and via crosstalk with other RNA specieslncRNAs can function as decoys, scaffolds, and enhancer RNAs This review summarizes the characteristics of lncRNAs, including their
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A typical workflow for identification and characterization of novel lncRNAs including the most commonly used methods is depicted in Fig 2Often, novel lncRNA targets are identified by RNAseq experiments either through de novo assembly or derived from an annotation database (eg, GENCODE , LNCipedia , NONCODE or Ensembl)Further characterization of lncRNAs, their isoforms and geneticComprehensive gene annotation ALL It contains the comprehensive gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes) This is a superset of the main annotation file;NONCODE (http//wwwbioinfoorg/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of noncoding RNAs (ncRNAs), especially long noncoding RNAs (lncRNAs) Since NONCODE 16 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of nextgeneration sequencing, which has produced an explosion of newly identified data
Molecular Traits Of Long Non Protein Coding Rnas From Diverse Plant Species Show Little Evidence Of Phylogenetic Relationships G3 Genes Genomes Genetics
Invited Review Long Non Coding Rnas Important Regulators In The Development Function And Disorders Of The Central Nervous System Cuevas Diaz Duran 19 Neuropathology And Applied Neurobiology Wiley Online Library
Expression profiles of long noncoding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability However, there lacks a comprehensive resource that systematically characterizes the expAuthors Fang, S, Zhang, L, Guo, J, et al (17) NONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res Yi Z, Hui L, Fang S, et al NONCODE 16 an informative and valuable data source of long noncoding RNAs J Nucleic Acids Research, 15, 44 (D1)D3D8Abstract Long noncoding RNAs (lncRNAs) are transcripts longer than 0 nucleotides with little or no protein coding potential The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research
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Long non‐coding RNAs (lncRNAs) refer to a class of non‐protein coding RNAs that are more than 0 nucleotides and are differentially accumulated in the nucleus and cytoplasm9 LncRNAs play various regulatory roles in the cell including regulation of development, stem cell pluripotency, cell growth and apoptosis and are frequentlyFunctional Analysis of Long NonCoding RNAs Functional Analysis of Long NonCoding RNAs pp Cite as Annotation of FullLength Long Noncoding RNAs with Capture LongRead Sequencing (CLS)Long noncoding RNAs (lncRNAs) are RNAs with a length of over 0 nucleotides that do not have proteincoding abilities Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases lncRNAs HNF1αAS1 and HNF4αAS1 are transcripts of lncRNA genes HNF1αAS1 and HNF4αAS1, which are antisense lncRNA genes located in the neighborhood regions of the
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Skeletal muscle long noncoding RNAs (lncRNAs) were reported to be involved in the development of type 2 diabetes (T2D) However, little is known about the mechanism of skeletal muscle lncRNAs on hyperglycemia of diabetic GotoKakizaki (GK) rats at the age of 3 and 4 weeks To elucidate this, we used RNAsequencing to profile the skeletal muscle transcriptomes including lncRNAs and mRNAs, inReason is that the functional annotation of long noncoding RNAs (lncRNAs) is largely missing LincRNAs comprise a heterogeneous subset of RNAs that are longer than 0 nucleotides (nt) and are transcribed from intergenic regions without proteincoding potential An increasing number of investigations haveINTRODUCTION There are vast majority of transcribed sequences that do not encode proteins called noncoding RNAs (ncRNAs) Long noncoding RNAs (lncRNAs) are ncRNAs that are >0 nt in length ()Many types of research showed that lncRNAs play key roles in different kinds of biological processes in animals, such as circuitry controlling pluripotency and differentiation, imprinting control
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GTF Long noncoding RNA gene annotation CHR It contains the comprehensive gene annotation of lncRNA genes on the referenceNONCODEV5 – a comprehensive annotation database for long noncoding RNAs November 17, 17 MNDR v – an updated resource of ncRNAdisease associations in mammalsNONCODE is a comprehensive database that aims to present the most complete collection and annotation of noncoding RNAs, especially long noncoding RNAs (lncRNA genes), and thus NONCODE is
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Danshen Transcriptional Resource Database (DsTRD) provides information on transcript sequences and functional annotations including proteincoding RNAs, lncRNAs, other ncRNA, miRNAs and phasiRNAs SoyFN is a resource about soybean miRNA functional networks and functional gene networks It also can be used to seek, download, and analyze the functional networks of soybean miRNAs andThe results bring us closer to a comprehensive annotation of human lncRNAs, though vast amounts of further work are needed to validate the predictions and fully decipher their biology NONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res (18) SA Mitra et al Several studies have shown that theNONCODE (http//wwwbioinfoorg/noncode/) is an interactive database that aims to present the most complete collection and annotation of noncoding RNAs, especially long noncoding RNAs (lncRNAs) The recently reduced cost of RNA sequencing has produced an explosion of newly identified data
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Annotation Of Full Length Long Noncoding Rnas With Capture Long Read Sequencing Cls Springerlink
NPInter v30 an upgraded database of noncoding RNssociated interactions NPInter v30 an upgraded database of noncoding RNssociated interactions NONCODEV5 a comprehensive annotation database for long noncoding RNAs NONCODEV5 a comprehensive annotation database for long noncoding RNAs FEELnc a tool for long noncoding RNANoncodev5 a comprehensive annotation database for long noncoding RNAs Nuclear Acids Res 46, D308–D314 doi /nar/gkx1107 PubMed Abstract CrossRef Full Text Google ScholarNONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res 18;
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NONCODE (http//wwwbioinfoorg/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of noncoding RNAs (ncRNAs), especially long noncoding RNAs (lncRNAs) Since NONCODE 16 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of nextgeneration sequencing, which has produced an explosion of newly identified dataAccumulating evidences have shown that long noncoding RNAs (lncRNAs) can act in cis or trans to perform diverse functions including regulating gene transcription and RNA splicing, modulating the activity or abundance of RNAs and proteins, and organizing nuclear domainsRunsheng Chen's 307 research works with 13,852 citations and 9,533 reads, including NONCODEV6 an updated database dedicated to long noncoding RNA annotation in both animals and plants
Invited Review Long Non Coding Rnas Important Regulators In The Development Function And Disorders Of The Central Nervous System Cuevas Diaz Duran 19 Neuropathology And Applied Neurobiology Wiley Online Library
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Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X NONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res 17;46(D1)D308–14 PubMedCentral CrossRef PubMed Google ScholarMammalian genomes contain tens of thousands of long noncoding RNAs (lncRNAs) that have been implicated in diverse biological processes However, the lncRNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts Based on RNPInter v30 an upgraded database of noncoding RNssociated interactions NPInter v30 an upgraded database of noncoding RNssociated interactions NONCODEV5 a comprehensive annotation database for long noncoding RNAs NONCODEV5 a comprehensive annotation database for long noncoding RNAs FEELnc a tool for long noncoding RNA
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Lnc2Cancer v updated database of experimentally supported long noncoding RNAs in human cancers Nucleic Acids Res 19 Jan 8;47(D1)D1028D1033 doi /nar/gky1096(ii) human exosome lncRNA expression profiles were displayed;NONCODE is a comprehensive database that aims to present the most complete collection and annotation of noncoding RNAs, especially long noncoding RNAs (lncRNA genes), and thus NONCODE is essential to modern biological and medical research Scientists are producing a flood of new data from which ne
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NONCODEV5 – a comprehensive annotation database for long noncoding RNAs November 17, 17 MNDR v – an updated resource of ncRNAdisease associations in mammalsNONCODE (current version v60) is an integrated knowledge database dedicated to noncoding RNAs (excluding tRNAs and rRNAs) NONCODE v5 is here MoreAndrogen receptor (AR)RNA complexes have been implicated in cancer, including melanoma Schmidt et al demonstrate that AR binds a single strand sequence in the long noncoding RNA (lncRNA) SLNCR Point mutations or oligonucleotides that abrogate AR binding to SLNCR block melanoma invasion, suggesting that targeting lncRNAprotein complexes holds therapeutic promise
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Data LNCipedia is a public database for long noncoding RNA (lncRNA) sequence and annotation The current release contains 127,802 transcripts and 56,946 genesBackground Long noncoding RNAs (lncRNAs) are transcripts that are 0 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown Results By exploiting available public EST databases, maize whole genome sequence annotation andExpression profiles of long noncoding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range
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Fang S, et al NONCODEV5 a comprehensive annotation database for long noncoding RNAs Nucleic Acids Res 18;46(Database issue)D308–14 Article Google ScholarDuring nuclear maturation of most eukaryotic premessenger RNAs and long noncoding RNAs, introns are removed through the process of RNA splicing Different classes of introns are excised by the U2type or the U12type spliceosomes, large complexes of small nuclear ribonucleoprotein particles and asA team led by researchers at the National Heart, Lung, and Blood Institute has assembled the most comprehensive long noncoding RNA knowledgebase (lncRNAKB) by methodically integrating widely used lncRNAs resources It presents the largest annotation of 77,199 human lncRNAs (224,286 transcripts) including the latest CHESS, FANTOM, LNCipedia, and NONCOD resources
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A comprehensive database that reveals lncRNA expression and variation among different cell groups is still lacking Table 1 List of selected scRNASeq databases NONCODEV5 a comprehensive annotation database for long noncoding RNAs Singlecell analysis of long noncoding RNAs in the developing human neocortexA comprehensive collection of 270,044 human lncRNAs and systematic curation of lncRNAs' annotation by multiomics data integration, function annotation and disease association MONOCLdb The MOuse NOnCode Lung database provides the annotations and expression profiles of mouse long noncoding RNAs (lncRNAs) involved in influenza and SARSCoVNONCODEV5 a comprehensive annotation database for long noncoding RNAs Fang S,Zhang L,Guo J,Niu Y,Wu Y,Li H,Zhao L,Li X,Teng X,Sun X,Sun L,Zhang MQ,Chen R,Zhao Y Nucleic Acids Res 17 View Paper (PubMed) View Publication
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Non Coding Rnas Long Non Coding Rnas And Micrornas In Endocrine Related Cancers In Endocrine Related Cancer Volume 25 Issue 4 18
Functional Analysis of Long NonCoding RNAs Functional Analysis of Long NonCoding RNAs pp Cite as Annotation of FullLength Long Noncoding RNAs with Capture LongRead Sequencing (CLS)Lnc2Cancer v updated database of experimentally supported long noncoding RNAs in human cancers Nucleic Acids Res 19 Jan 8;47(D1)D1028D1033 doi /nar/gky109646 D308D314 View in Article
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