ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web

Fucile, Geoffrey; Biase, David Di; Nahal, Hardeep; La, Garon; Khodabandeh, S; Yani, Chen; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence A.; Provart, Nicholas J.

doi:10.1371/journal.pone.0015237

Cited by 49 publications

(32 citation statements)

References 67 publications

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“…There are many nonsynonymous SNPs that occur in just one ecotype that we hypothesize to be of less functional importance than those that are found in several ecotypes. This sort of analysis was not possible with the prototypic ePlant interface released several years ago (Fucile et al, 2011). Not having to switch windows and contend with several different user interfaces to explore an idea from multiple perspectives should liberate researchers and make it easier to stay "on task" and make creative associations without distraction.…”

Section: Discussionmentioning

confidence: 99%

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%

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

et al. 2017

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“…Sequences of GH1 from all 15 Arabidopsis GH1-containing proteins were used as queries. All records found are included in Table I and Supplemental Table S1 (Fucile et al 2011). Additionally, the full genomic sequence from TAIR repository was translated in six reading frames and searched by position-specific iterated BLAST (Altschul et al, 1997).…”

Section: Database Screenmentioning

confidence: 99%

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain

Kotliński

Kniżewski²,

Muszewska³

et al. 2017

Plant Physiol.

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(A.J.).H1 (or linker) histones are basic nuclear proteins that possess an evolutionarily conserved nucleosome-binding globular domain, GH1. They perform critical functions in determining the accessibility of chromatin DNA to trans-acting factors. In most metazoan species studied so far, linker histones are highly heterogenous, with numerous nonallelic variants cooccurring in the same cells. The phylogenetic relationships among these variants as well as their structural and functional properties have been relatively well established. This contrasts markedly with the rather limited knowledge concerning the phylogeny and structural and functional roles of an unusually diverse group of GH1-containing proteins in plants. The dearth of information and the lack of a coherent phylogeny-based nomenclature of these proteins can lead to misunderstandings regarding their identity and possible relationships, thereby hampering plant chromatin research. Based on published data and our in silico and highthroughput analyses, we propose a systematization and coherent nomenclature of GH1-containing proteins of Arabidopsis (Arabidopsis thaliana [L.] Heynh) that will be useful for both the identification and structural and functional characterization of homologous proteins from other plant species.

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“…Expression of AtSCC2, AtSCC4, SYN1, SYN2, SYN3 and SYN4 in Arabidopsis tissues was estimated by using the Anatomy tool of the GENEVESTIGATOR database (https://www.genevestigator.com; Zimmermann et al, 2004) and the spatiotemporal expression tool of the eFP browser (http://bar.utoronto.ca/ dev/eplant/; Fucile et al, 2011).…”

Section: In Silico Expression Analysismentioning

confidence: 99%

The Arabidopsis homolog of Scc4/MAU2 is essential for embryogenesis

Minina¹,

Reza²,

Gutiérrez-Beltrán³

et al. 2017

Development

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Factors regulating dynamics of chromatin structure have direct impact on expression of genetic information. Cohesin is a multi-subunit protein complex that is crucial for pairing sister chromatids during cell division, DNA repair and regulation of gene transcription and silencing. In non-plant species, cohesin is loaded on chromatin by the Scc2-Scc4 complex (also known as the NIBPL-MAU2 complex). Here, we identify the Arabidopsis homolog of Scc4, which we denote Arabidopsis thaliana (At)SCC4, and show that it forms a functional complex with AtSCC2, the homolog of Scc2. We demonstrate that AtSCC2 and AtSCC4 act in the same pathway, and that both proteins are indispensable for cell fate determination during early stages of embryo development. Mutant embryos lacking either of these proteins develop only up to the globular stage, and show the suspensor overproliferation phenotype preceded by ectopic auxin maxima distribution. We further establish a new assay to reveal the AtSCC4-dependent dynamics of cohesin loading on chromatin in vivo. Our findings define the Scc2-Scc4 complex as an evolutionary conserved machinery controlling cohesin loading and chromatin structure maintenance, and provide new insight into the plant-specific role of this complex in controlling cell fate during embryogenesis.

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ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web

Cited by 49 publications

References 67 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

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain

The Arabidopsis homolog of Scc4/MAU2 is essential for embryogenesis

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