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NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome.

Bostan H, Chiusano ML - BMC Plant Biol. (2015)

Bottom Line: However, although the flourishing of tools to process the NGS data, versatile and user-friendly computational environments for integrative and comparative analyses of the results from the increasing amount of collections are still required.Here we present the architecture and the facilities of NexGenEx-, a web based platform that offers processed NGS transcriptome collections and enables immediate analyses of the results.The platform is proposed as an example effort in tomato, and is described as a profitable approach for the exploitation of these challenging and precious datasets.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Next Generation Sequencing technologies (NGS) unexpectedly pushed forward the capability of solving genome organization and of widely depicting gene expression. However, although the flourishing of tools to process the NGS data, versatile and user-friendly computational environments for integrative and comparative analyses of the results from the increasing amount of collections are still required.

Description: Here we present the architecture and the facilities of NexGenEx-, a web based platform that offers processed NGS transcriptome collections and enables immediate analyses of the results. The platform allows gene expression investigations, profiling and comparisons, and exploits different resources.

Conclusion: In the current version, NexGenEx-Tom includes processed and normalized NGS expression data from three collections covering several tissue/stages from different genotypes. Beyond providing a user-friendly interface, the platform was designed with the aim to easily be expanded to include other NGS based transcriptome collections. It can also integrate different genome releases, possibly from different cultivars or genotypes, but even from different species. The platform is proposed as an example effort in tomato, and is described as a profitable approach for the exploitation of these challenging and precious datasets.

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Snapshots of results provided by the platform: A) example query; B) accordion view of all results; C) expression matrix and profiling; D) correlation matrix; E) expression profiling plot; F) functional annotation and locus position on the genome; G) GO Terms summary table; H) GO Terms association table and I) Locus overview from all collections.
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Related In: Results  -  Collection

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Fig3: Snapshots of results provided by the platform: A) example query; B) accordion view of all results; C) expression matrix and profiling; D) correlation matrix; E) expression profiling plot; F) functional annotation and locus position on the genome; G) GO Terms summary table; H) GO Terms association table and I) Locus overview from all collections.

Mentions: In FigureĀ 3, an example query including a list of 5 gene IDs and the corresponding result views are shown.Figure 3


NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome.

Bostan H, Chiusano ML - BMC Plant Biol. (2015)

Snapshots of results provided by the platform: A) example query; B) accordion view of all results; C) expression matrix and profiling; D) correlation matrix; E) expression profiling plot; F) functional annotation and locus position on the genome; G) GO Terms summary table; H) GO Terms association table and I) Locus overview from all collections.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4340097&req=5

Fig3: Snapshots of results provided by the platform: A) example query; B) accordion view of all results; C) expression matrix and profiling; D) correlation matrix; E) expression profiling plot; F) functional annotation and locus position on the genome; G) GO Terms summary table; H) GO Terms association table and I) Locus overview from all collections.
Mentions: In FigureĀ 3, an example query including a list of 5 gene IDs and the corresponding result views are shown.Figure 3

Bottom Line: However, although the flourishing of tools to process the NGS data, versatile and user-friendly computational environments for integrative and comparative analyses of the results from the increasing amount of collections are still required.Here we present the architecture and the facilities of NexGenEx-, a web based platform that offers processed NGS transcriptome collections and enables immediate analyses of the results.The platform is proposed as an example effort in tomato, and is described as a profitable approach for the exploitation of these challenging and precious datasets.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Next Generation Sequencing technologies (NGS) unexpectedly pushed forward the capability of solving genome organization and of widely depicting gene expression. However, although the flourishing of tools to process the NGS data, versatile and user-friendly computational environments for integrative and comparative analyses of the results from the increasing amount of collections are still required.

Description: Here we present the architecture and the facilities of NexGenEx-, a web based platform that offers processed NGS transcriptome collections and enables immediate analyses of the results. The platform allows gene expression investigations, profiling and comparisons, and exploits different resources.

Conclusion: In the current version, NexGenEx-Tom includes processed and normalized NGS expression data from three collections covering several tissue/stages from different genotypes. Beyond providing a user-friendly interface, the platform was designed with the aim to easily be expanded to include other NGS based transcriptome collections. It can also integrate different genome releases, possibly from different cultivars or genotypes, but even from different species. The platform is proposed as an example effort in tomato, and is described as a profitable approach for the exploitation of these challenging and precious datasets.

Show MeSH