Literature DB >> 23476021

PLncDB: plant long non-coding RNA database.

Jingjing Jin1, Jun Liu, Huan Wang, Limsoon Wong, Nam-Hai Chua.   

Abstract

SUMMARY: Plant long non-coding RNA database (PLncDB) attempts to provide the following functions related to long non-coding RNAs (lncRNAs): (i) Genomic information for a large number of lncRNAs collected from various resources; (ii) an online genome browser for plant lncRNAs based on a platform similar to that of the UCSC Genome Browser; (iii) Integration of transcriptome datasets derived from various samples including different tissues, developmental stages, mutants and stress treatments; and (iv) A list of epigenetic modification datasets and small RNA datasets. Currently, our PLncDB provides a comprehensive genomic view of Arabidopsis lncRNAs for the plant research community. This database will be regularly updated with new plant genome when available so as to greatly facilitate future investigations on plant lncRNAs. AVAILABILITY: PLncDB is freely accessible at http://chualab.rockefeller.edu/gbrowse2/homepage.html and all results can be downloaded for free at the website.

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Year:  2013        PMID： 23476021      PMCID： PMC3624813          DOI： 10.1093/bioinformatics/btt107

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  37 in total

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Journal:  Genome Res       Date:  2008-06-18       Impact factor: 9.043

2.  In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula.

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Journal:  In Silico Biol       Date:  2007

Review 3.  Diamonds in the rough: mRNA-like non-coding RNAs.

Authors:  Linda A Rymarquis; James P Kastenmayer; Alexander G Hüttenhofer; Pamela J Green
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4.  Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster.

Authors:  Jonathan L Tupy; Adina M Bailey; Gina Dailey; Martha Evans-Holm; Christian W Siebel; Sima Misra; Susan E Celniker; Gerald M Rubin
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-04       Impact factor: 11.205

5.  Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array.

Authors:  Akihiro Matsui; Junko Ishida; Taeko Morosawa; Yoshiki Mochizuki; Eli Kaminuma; Takaho A Endo; Masanori Okamoto; Eiji Nambara; Maiko Nakajima; Makiko Kawashima; Masakazu Satou; Jong-Myong Kim; Norio Kobayashi; Tetsuro Toyoda; Kazuo Shinozaki; Motoaki Seki
Journal:  Plant Cell Physiol       Date:  2008-07-13       Impact factor: 4.927

6.  Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.

Authors:  Xiu-Jie Wang; Terry Gaasterland; Nam-Hai Chua
Journal:  Genome Biol       Date:  2005-03-15       Impact factor: 13.583

7.  NRED: a database of long noncoding RNA expression.

Authors:  Marcel E Dinger; Ken C Pang; Tim R Mercer; Mark L Crowe; Sean M Grimmond; John S Mattick
Journal:  Nucleic Acids Res       Date:  2008-10-01       Impact factor: 16.971

8.  Computational prediction of novel non-coding RNAs in Arabidopsis thaliana.

Authors:  Dandan Song; Yang Yang; Bin Yu; Binglian Zheng; Zhidong Deng; Bao-Liang Lu; Xuemei Chen; Tao Jiang
Journal:  BMC Bioinformatics       Date:  2009-01-30       Impact factor: 3.169

9.  The Arabidopsis Information Resource (TAIR): gene structure and function annotation.

Authors:  David Swarbreck; Christopher Wilks; Philippe Lamesch; Tanya Z Berardini; Margarita Garcia-Hernandez; Hartmut Foerster; Donghui Li; Tom Meyer; Robert Muller; Larry Ploetz; Amie Radenbaugh; Shanker Singh; Vanessa Swing; Christophe Tissier; Peifen Zhang; Eva Huala
Journal:  Nucleic Acids Res       Date:  2007-11-05       Impact factor: 16.971

10.  Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis.

Authors:  Sookyung Oh; Sunchung Park; Steven van Nocker
Journal:  PLoS Genet       Date:  2008-08-22       Impact factor: 5.917
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  65 in total

1.  Identification of alternatively spliced gene isoforms and novel noncoding RNAs by single-molecule long-read sequencing in Camellia.

Authors:  Zhikang Hu; Tao Lyu; Chao Yan; Yupeng Wang; Ning Ye; Zhengqi Fan; Xinlei Li; Jiyuan Li; Hengfu Yin
Journal:  RNA Biol       Date:  2020-03-19       Impact factor: 4.652

2.  Genome-wide identification of long non-coding RNA targets of the tomato MADS box transcription factor RIN and function analysis.

Authors:  Tongtong Yu; David T W Tzeng; Ran Li; Jianye Chen; Silin Zhong; Daqi Fu; Benzhong Zhu; Yunbo Luo; Hongliang Zhu
Journal:  Ann Bot       Date:  2019-02-15       Impact factor: 4.357

3.  Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.

Authors:  Jules Deforges; Rodrigo S Reis; Philippe Jacquet; Shaoline Sheppard; Veerendra P Gadekar; Gene Hart-Smith; Andrea Tanzer; Ivo L Hofacker; Christian Iseli; Ioannis Xenarios; Yves Poirier
Journal:  Plant Physiol       Date:  2019-02-13       Impact factor: 8.340

4.  High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.

Authors:  Song Li; Masashi Yamada; Xinwei Han; Uwe Ohler; Philip N Benfey
Journal:  Dev Cell       Date:  2016-11-10       Impact factor: 12.270

Review 5.  Long Noncoding RNAs in Plants.

Authors:  Hsiao-Lin V Wang; Julia A Chekanova
Journal:  Adv Exp Med Biol       Date:  2017       Impact factor: 2.622

6.  The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome.

Authors:  Agnieszka A Golicz; Mohan B Singh; Prem L Bhalla
Journal:  Plant Physiol       Date:  2017-12-28       Impact factor: 8.340

7.  Long non-coding RNAs: a novel endogenous source for the generation of Dicer-like 1-dependent small RNAs in Arabidopsis thaliana.

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8.  Transcriptome-wide identification and functional investigation of the RDR2- and DCL3-dependent small RNAs encoded by long non-coding RNAs in Arabidopsis thaliana.

Authors:  Zhonghai Tang; Min Xu; Jiahui Cai; Xiaoxia Ma; Jingping Qin; Yijun Meng
Journal:  Plant Signal Behav       Date:  2019-05-13

9.  Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza.

Authors:  Dongqiao Li; Fenjuan Shao; Shanfa Lu
Journal:  Planta       Date:  2015-01-20       Impact factor: 4.116

10.  CURLY LEAF Regulates Gene Sets Coordinating Seed Size and Lipid Biosynthesis.

Authors:  Jun Liu; Shulin Deng; Huan Wang; Jian Ye; Hui-Wen Wu; Hai-Xi Sun; Nam-Hai Chua
Journal:  Plant Physiol       Date:  2016-03-04       Impact factor: 8.340
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