Araport: the Arabidopsis Information Portal

Krishnakumar, Vivek; Hanlon, Matthew; Contrino, Sergio; Ferlanti, Erik S.; Karamycheva, Svetlana; Maria, Kim; Rosen, Benjamin D.; Cheng, Chia Yi; Moreira, Wálter; Mock, Stephen; Stubbs, Joe; Sullivan, Julie; Krampis, Konstantinos; Miller, Jason R.; Micklem, Gos; Vaughn, Matthew; Town, Christopher D.

doi:10.1093/nar/gku1200

Cited by 186 publications

(165 citation statements)

References 29 publications

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“…We have successfully deployed ePlant on the new international portal for Arabidopsis information, Araport.org (Krishnakumar et al, 2015). This is a large collaborative effort that demonstrates the power of a federated web service-based approach in integrating and visualizing data from multiple sources, as articulated by the International Arabidopsis Informatics Consortium (2012).…”

Section: Discussionmentioning

confidence: 99%

“…Immediately beneath it, the Publications Viewer ( Figure 4B) provides a list of publications and gene "reference into function" records (GeneRIFs) about the currently selected gene, along with links to the actual papers on PubMed. Both are powered by web services from Araport (Krishnakumar et al, 2015). These modules are atypical for ePlant because they are primarily text based.…”

Section: Gene Information and Publications Viewermentioning

confidence: 99%

“…The 3D model (structure models have been computed for 23,091 Arabidopsis gene products as part of the ePlant effort) comes from Phyre2 (Kelley et al, 2015) and data layers include (1) complete protein sequences from Araport (Krishnakumar et al, 2015); (2) nonsynonymous SNP locations in the underlying gene sequence from the 1001 Proteomes project (Joshi et al, 2011) with a list of which ecotypes in which they are found; (3) Pfam domains (Finn et al, 2014); and (4) CDD feature hits (Marchler-Bauer et al, 2015). Drawing this information onto the 3D molecular structure enables researchers to visualize exactly where in the physical model of the protein such features exist.…”

Section: Molecule Viewermentioning

confidence: 99%

“…They also facilitate comparison of multiple levels of data from a variety of sources (e.g., methylation, phosphorylation, SNPs, This module ( Figure 2H) uses an implementation of JBrowse (Skinner et al, 2009) using data provided by web services at Araport (Krishnakumar et al, 2015). Due to the complexity of the program, we did not apply the ePlant style guide to this tool so there is some perceptual difference between this and the other ePlant modules.…”

Section: Sequence Viewermentioning

confidence: 99%

“…A thorough investigation of ABI3 would require visiting Araport (Krishnakumar et al, 2015) or TAIR (Berardini et al, 2015) for annotation and sequence information, the BAR Arabidopsis Interactions Viewer (Geisler-Lee et al, 2007) or BioGRID (ChatrAryamontri et al, 2015) for protein-protein interactions, SUBA3 (Tanz et al, 2013) for subcellular localization information, Phyre2 (Kelley et al, 2015) for 3D molecular models, Reactome (Joshi-Tope et al, 2005) for signal, metabolic, and gene regulation pathway charts, and dozens of other sites, each dedicated to their own particular layer of analysis.…”

Section: Introductionmentioning

confidence: 99%

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ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

et al. 2017

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A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research

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Section: Discussionmentioning

confidence: 99%

Section: Gene Information and Publications Viewermentioning

confidence: 99%

Section: Molecule Viewermentioning

confidence: 99%

Section: Sequence Viewermentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

et al. 2017

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Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual

Sanderson

Park

Jameel

et al. 2019

American J of Botany

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Premise Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Italy and Sweden provides an essential foundation for uncovering the genotype–phenotype–fitness map for an adaptive response to a key environmental stress. Methods We examined the consequences of a naturally occurring loss‐of‐function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing‐tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing the Italian CBF2 allele, and two contained deletions created using CRISPR‐Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation. Results Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which all CBF2 LOF lines, and the IT ecotype had similar patterns of reduced cold responsive expression compared to the SW ecotype. Conclusions We identified 10 genes that are at least partially regulated by CBF2 that may contribute to the differences in cold‐acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.

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Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes

Reiser

Subramaniam

et al. 2017

CP in Bioinformatics

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The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, orthologs, gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of Web-based search and display tools. This unit primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes and genome. Additionally, we describe how members of the community can share data using TAIR's Online Annotation Submission Tool (TOAST), in order to make their published research more accessible and visible. © 2017 by John Wiley & Sons, Inc.

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Araport: the Arabidopsis Information Portal

Cited by 186 publications

References 29 publications

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual

Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes

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