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Protocols

PlantPAN specifications

Information


Unique identifier OMICS_32908
Name PlantPAN
Alternative name Plant Promoter Analysis Navigator
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 3.0
Maintained Yes

Maintainer


  • person_outline Wen-Chi Chang

Additional information


http://plantpan.itps.ncku.edu.tw/index.html#guide The version 2.0 of the database is available at http://plantpan2.itps.ncku.edu.tw/

Publications for Plant Promoter Analysis Navigator

PlantPAN citations

 (20)
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Multifunctional activities of ERF109 as affected by salt stress in Arabidopsis

2018
Sci Rep
PMCID: 5913302
PMID: 29686365
DOI: 10.1038/s41598-018-24452-6
call_split See protocol

[…] Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.ad.jp/kegg/)–. Analysis of promoter cis-elements for the genes in the first four clusters was done using Promoter Analysis software (http://plantpan2.itps.ncku.edu.tw/promoter.php) consulting the promoter sequence (up to −500 nt) datasets available at TAIR in order to detect putative binding sites for ERF109 and other TFs in the AP2/ERF g […]

call_split

The FBH family of bHLH transcription factors controls ACC synthase expression in sugarcane

2018
J Exp Bot
PMCID: 5920332
PMID: 29514290
DOI: 10.1093/jxb/ery083
call_split See protocol

[…] elements present in at least three different species, including sugarcane, were considered in the search for putative transcription factor binding sites (TFBS). We identified putative TFBS using the PlantPAN 2.0 database (), and the resulting cis-element sequences were manually double-checked against original references; elements containing inconsistencies were discarded. […]

library_books

Ubiquitin related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

2018
BMC Plant Biol
PMCID: 5784548
PMID: 29370763
DOI: 10.1186/s12870-018-1241-5

[…] Transcripts with < 1000 bp upstream in the reference sequence were not used in the analysis. We used the FIMO tool from the MEME suite (v 4.11.4; []) with a position weight matrix (PWM) obtained from plantPAN 2.0 (http://plantpan2.itps.ncku.edu.tw/; []). We ran FIMO with a p value threshold of <1e-4 (default), increased the max-stored-scores to 1,000,000 to account for the size of the dataset, and […]

library_books

Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice

2017
Front Plant Sci
PMCID: 5693882
PMID: 29181013
DOI: 10.3389/fpls.2017.01944

[…] du.cn) was used to analyze the gene structure and for calculating the number of exon and intron in the gene sequence. The cis-acting elements in the promoter region of OsGATA genes were deduced using PlantPan version 2 (http://plantpan2.itps.ncku.edu.tw/). […]

library_books

Identification of miRNA mediated drought responsive multi tiered regulatory network in drought tolerant rice, Nagina 22

2017
Sci Rep
PMCID: 5684420
PMID: 29133823
DOI: 10.1038/s41598-017-15450-1

[…] rther the promoter sequences from N22 were analyzed for the presence of cis-regulatory elements using PLACE database (http://www.dna.affrc.go.jp/PLACE/) and the OsSPL9 binding sites were mapped using PlantPAN 2.0. […]

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Dataset of the HOX1 gene sequences of the wheat polyploids and their diploid relatives

2017
PMCID: 5699892
PMID: 29201982
DOI: 10.1016/j.dib.2017.11.010
call_split See protocol

[…] nment of a selective set of structurally different amino acid sequences for each species (). The putative cis- regulatory, stress responsive elements in the gene promoter were searched using database PlantPAN 2.0 (http://plantpan2.itps.ncku.edu.tw). represents the most conservative elements implicated in response to drought and/or abscisic acid (ABA) which triggers ABA signaling pathway associate […]

Citations

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PlantPAN institution(s)
Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan; School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China; Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
PlantPAN funding source(s)
Supported by Ministry of Science and Technology [MOST 105-2311-B006-004-MY3]; Academia Sinica (Innovative Translational Agricultural Research Grant).

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