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PlantGenIE specifications

Information


Unique identifier OMICS_28173
Name PlantGenIE
Alternative name Plant Genome Integrative Explorer
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Nathaniel Street

Publication for Plant Genome Integrative Explorer

PlantGenIE citations

 (6)
library_books

Ethylene Related Gene Expression Networks in Wood Formation

2018
Front Plant Sci
PMCID: 5861219
PMID: 29593753
DOI: 10.3389/fpls.2018.00272

[…] The gene family members of ethylene receptor, CTR1, EIN2, EIN3, and ERF genes of A. thaliana, P. trichocarpa and P. abies were extracted from the Plant Genome Integrative Explorer resource (PlantGenIE.org; Sundell et al., ; Gene Family tab). In order to find homologous gene models putatively placed in separate gene families and P. abies full-le […]

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Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803

2017
Nucleic Acids Res
PMCID: 5714215
PMID: 29036481
DOI: 10.1093/nar/gkx860

[…] pletion and nitrogen starvation. An adjusted P-value of <0.1 was considered to be significant. For Gene Ontology (GO) enrichment analysis, the GSEA tool () and Synergy () (available at http://synergy.plantgenie.org), were applied. Network construction and visualisation were carried out using Cytoscape 3.2.0 ().Hierarchical complete-linkage clustering was performed with Cluster 3.0 (). Clusters wer […]

library_books

Gene co expression network connectivity is an important determinant of selective constraint

2017
PLoS Genet
PMCID: 5407845
PMID: 28406900
DOI: 10.1371/journal.pgen.1006402

[…] Stockholm, Sweden. Raw data is available at the European Nucleotide Archive (ENA, []) with accession number ERP014886, and the normalised and filtered gene expression data matrix is available at the PlantGenIE FTP resource (ftp://plantgenie.org/Publications/Maehler2016/).RNA-Seq FASTQ-files were pre-processed and aligned to v1.0 of the P. tremula reference genome [] as in []. In short, reads were […]

library_books

Computational Tools for Genomic Studies in Plants

2016
Curr Genomics
PMCID: 5282602
PMID: 28217007
DOI: 10.2174/1389202917666160520103447

[…] database is currently active and permits identify groups of related genes and their expression patterns, using the microarray information existing at the date the current version was released. 3.11. PlantGenIE.org [] is a collection of web resources for searching, visualizing and analyzing genomics and transcriptomics data recently developed for different plant species. Currently, it includes ded […]

library_books

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

2016
PMCID: 5144951
PMID: 27799338
DOI: 10.1534/g3.116.032805

[…] rieved from the PLAZA (v3.0) set (), pine sequences from the PineRefSeq project (http://dendrome.ucdavis.edu/ftp/Genome_Data/genome/pinerefseq/), and spruce sequences from the Congenie project (ftp://plantgenie.org/Data/ConGenIE/) (). All protein sequences were clustered at 95% identity with USEARCH-UCLUST. Subsequently, pairwise NCBI BLAST v2.2.29+ (E-value 1eāˆ’05) was run against the clustered se […]

library_books

An Ancient Transkingdom Horizontal Transfer of Penelope Like Retroelements from Arthropods to Conifers

2016
Genome Biol Evol
PMCID: 4860704
PMID: 27190138
DOI: 10.1093/gbe/evw076

[…] ruce were downloaded from the TreeGenes () ftp website (http://dendrome.ucdavis.edu/ftp/Genome_Data/genome/pinerefseq/Pita/transcriptome/, last accessed April 6, 2016) and the Congenie website (ftp://plantgenie.org/ConGenIE/, last accessed April 6, 2016), respectively. To identify and retrieve Dryad elements and EN(āˆ’)PLEs from these genomes, we first performed tBLASTn (default settings except e-va […]

Citations

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PlantGenIE institution(s)
Umea Plant Science Centre, Department of Plant Physiology, Umea University, Umea, Sweden; Computational Life Science Cluster (CLiC), Umea University, Umea, Sweden; Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Department of Chemistry, Umea University, Umea, Sweden; Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
PlantGenIE funding source(s)
Supported by This work was supported by funds from the Alice Wallenberg Foundation, the Swedish Research Council (VR), the Swedish Governmental Agency for Innovation Systems (Vinnova), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas), and the Swedish Foundation for Strategic Research (SSF), in part through the UPSC Berzelii Centre for Forest Biotechnology.

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