MeV: MultiExperiment Viewer

Howe, Eleanor; Holton, Kristina M.; Nair, Sarita J.; Schlauch, Daniel; Sinha, Raktim; Quackenbush, John

doi:10.1007/978-1-4419-5714-6_15

Cited by 235 publications

(185 citation statements)

References 17 publications

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“…A BLASTp search was also computed with the same parameters against the clusters of orthologous groups of proteins of the nucleocytoplasmic large DNA virus (NCVOGs) [22]. A cladistic representation based on the presence/absence of each NCVOG was performed by MultiExperiment Viewer (MeV) [23]. Conserved domains and putative functions of viral proteins were predicted by comparative genomics through a BLASTp search against the NCBI non-redundant protein sequence database and by using InterPro v58.0 (); results merged with specific Delta-BLAST results [24].…”

Section: Methodsmentioning

confidence: 99%

Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses

Andréani

Aherfi

Khalil

et al. 2016

Viruses

118

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Most viruses are known for the ability to cause symptomatic diseases in humans and other animals. The discovery of Acanthamoeba polyphaga mimivirus and other giant amoebal viruses revealed a considerable and previously unknown area of uncharacterized viral particles. Giant viruses have been isolated from various environmental samples collected from very distant geographic places, revealing a ubiquitous distribution. Their morphological and genomic features are fundamental elements for classifying them. Herein, we report the isolation and draft genome of Cedratvirus, a new amoebal giant virus isolated in Acanthamoeba castellanii, from an Algerian environmental sample. The viral particles are ovoid-shaped, resembling Pithovirus sibericum, but differing notably in the presence of two corks at each extremity of the virion. The draft genome of Cedratvirus—589,068 base pairs in length—is a close relative of the two previously described pithoviruses, sharing 104 and 113 genes with P. sibericum and Pithovirus massiliensis genomes, respectively. Interestingly, analysis of these viruses’ core genome reveals that only 21% of Cedratvirus genes are involved in best reciprocal hits with the two pithoviruses. Phylogeny reconstructions and comparative genomics indicate that Cedratvirus is most closely related to pithoviruses, and questions their membership in an enlarged putative Pithoviridae family.

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Section: Methodsmentioning

confidence: 99%

Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses

Andréani

Aherfi

Khalil

et al. 2016

Viruses

118

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“…For effective comparison, we also obtained the top-10 most enriched Gene Ontology MultipleExperiment Viewer (MeV, a software package for displays of high throughput analysis) [44]. Clear distinction was observed between MA genes and the rest, in which the MA-alone genes were uniquely enriched in cell surface and secretion related biological processes including "cell-cell signaling", "defense response", "regulation of response to external stimulus", and "regulation of hormone levels".…”

Section: Functional Analysismentioning

confidence: 99%

Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis

Zhang

Akintola

Liu

et al. 2016

Gene

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“…The computational approach started with ANOVA to identify nitrogen regulated genes (Type 1 algorithm). Next, MeV software [125] was used to separate the nitrogen regulated genes into 20 clusters, eight of which appeared to have over-represented biological functions (Type 2 algorithm). The application of LASSO based algorithm to cluster representatives provided coefficients for a system of linear ODEs describing the dynamics of each cluster (Type 5 algorithm).…”

Section: Gene Relationship Inferencementioning

confidence: 99%

Computational approaches to identify regulators of plant stress response using high-throughput gene expression data

Koryachko

Matthiadis

Ducoste

et al. 2015

Current Plant Biology

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a b s t r a c tInsight into biological stress regulatory pathways can be derived from high-throughput transcriptomic data using computational algorithms. These algorithms can be integrated into a computational approach to provide specific testable predictions that answer biological questions of interest. This review conceptually organizes a wide variety of developed algorithms into a classification system based on desired type of output predictions. This classification is then used as a structure to describe completed approaches in the literature, with a focus on project goals, overall path of implemented algorithms, and biological insight gained. These algorithms and approaches are introduced mainly in the context of research on the model plant species Arabidopsis thaliana under stress conditions, though the nature of computational techniques makes these approaches easily applicable to a wide range of species, data types, and conditions.

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MeV: MultiExperiment Viewer

Cited by 235 publications

References 17 publications

Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses

Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses

Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis

Computational approaches to identify regulators of plant stress response using high-throughput gene expression data

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