Arabidopsis eFP Browser protocols

View Arabidopsis eFP Browser computational protocol

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Arabidopsis eFP Browser specifications

Information


Unique identifier OMICS_22410
Name Arabidopsis eFP Browser
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • Arabidopsis Seed Coat eFP Browser

Maintainer


  • person_outline Nicholas J. Provart <>

Additional information


http://bar.utoronto.ca/efp_seedcoat/cgi-bin/efpWeb.cgi

Publication for Arabidopsis eFP Browser

Arabidopsis eFP Browser in pipelines

 (4)
2017
PMCID: 5545994
PMID: 28786034
DOI: 10.1186/s12284-017-0177-y

[…] (plant microrna knowledge base) (meng et al., ), mirex (arabidopsis pri-mirna expression atlas) (bielewicz et al., ), avt (atgenexpress visualization tool) (kilian et al., ; goda et al., ), and arabidopsis efp browser (winter et al., ). the biological functions of the srna target genes could be analyzed by using agrigo (du et al., )., in the present work, we proposed a general workflow […]

2015
PMCID: 4431829
PMID: 25974423
DOI: 10.1371/journal.pone.0125624

[…] consistent with data from publicly available expression databases (). transcriptomics analysis using genecat (http://genecat.mpg.de) [], genevestigator (http://www.genevestigator.com/gv/) [] and the arabidopsis efp browser (http://bar.utoronto.ca/efp/cgi-bin/efpweb.cgi) [] indicate both genes are widely expressed with galt5 having a higher overall expression compared to galt2. it is also […]

2015
PMCID: 4469908
PMID: 25997736
DOI: 10.14348/molcells.2015.2323

[…] category “pollen development process (go:0009555)” were highly represented (p value = 1.30e–11), which included 32 genes ( and ). the expression patterns of these 32 genes were reconstructed using arabidopsis efp browser (http://bar.utoronto.ca/efp/cgi-bin/efpweb.cgi) () (). all of these genes, as well as askβ, were highly expressed in tricellular and mature stage pollen grains, […]

2013
PMCID: 3797442
PMID: 24137171
DOI: 10.3389/fpls.2013.00406

[…] are expressed at low levels in siliques and mature leaves, while attcp22 is not detected in inflorescences and mature leaves (figure ). expression data from genevestigator (hruz et al., ), the arabidopsis efp browser at bar (winter et al., ), atgenexpress (schmid et al., ), and genecat (mutwil et al., ) supports our rt-pcr analysis for attcp8, attcp14, attcp15, attcp21, and attcp23, […]


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Arabidopsis eFP Browser in publications

 (130)
PMCID: 5855860
PMID: 29495267
DOI: 10.3390/ijms19020638

[…] symptoms in leaves of both plants types (b). these results indicate that increased expression of rtnlb3 and 8 may lead to enhanced susceptibility to pst dc3000 infection., a previous study using the arabidopsis efp browser suggested that rtnlb1-4 and 13 genes have tissue-specific expression patterns and levels [,]. to understand other functions of rtnlbs in plants, we used quantitative real-time […]

PMCID: 5805785
PMID: 29422671
DOI: 10.1038/s41467-018-03013-5

[…] being specialized for accumulation of mucilage constituents and starch granules (fig. , right panels). these gus staining patterns in seeds are generally consistent with the expression data from the arabidopsis efp browser– (fig.  and supplementary fig. ). notably, robust expression of sk11 and sk12 in maternal tissues of seeds, such as the chalaza and integument, overlapped with strong ttg1 […]

PMCID: 5742180
PMID: 29312925
DOI: 10.3389/fchem.2017.00115

[…] the drought-related expression of cdpk genes was examined using available published water deficit microarray studies. for arabidopsis, geo datasets gse76827, gse55431, and arabidopsis efp browser containing data of root, shoot, and leaves in different time point and days were used. for maize, drought expression data of root, stem leaf, cob, and tassel was collected […]

PMCID: 5703579
PMID: 29131815
DOI: 10.1371/journal.pgen.1007076

[…] in identifying the degs []. the raw microarray data and detailed protocol were deposited in the gene expression omnibus database (gse90622). when necessary, mapman (http://mapman.gabipd.org), or arabidopsis efp browser (http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpweb.cgi) were used to analyze the data., total rna was extracted using trizol reagent (invitrogen). previously described […]

PMCID: 5660992
PMID: 29118774
DOI: 10.3389/fpls.2017.01812

[…] from the phylogenetic reconstruction were calculated., the atgenexpress expression data of a. thaliana bg and bgl genes in different developmental stages and auxin treatments were retrieved from arabidopsis efp browser (; ; ). the response of bg and bgl genes towards auxin treatments were calculated from this data. the values were plotted as heat maps using multiexperiment viewer (mev, v4.8) […]


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Arabidopsis eFP Browser institution(s)
Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada
Arabidopsis eFP Browser funding source(s)
Supported in part by grants from Genome Canada and NSERC, the Natural Sciences and Engineering Research Council of Canada (NSERC).

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