ExpressWeb: A Web application for clustering and visualization of expression data

Savelli, Bruno; Picard, Serge; Roux, Christophe; Dunand, Christophe

doi:10.1101/625939

Cited by 3 publications

(2 citation statements)

References 8 publications

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“…This requires the availability of genomic localization for larger number of organisms. In addition, we have recently developed ExpressWeb, an online tool to perform gene clustering using personal or selected expressed value sets in order to construct co-expression gene networks [26]. ExpressWeb is available directly from the RedoxiBase and a current priority is to set up a pipeline to load publicly available expression data in order to perform expression clustering with our favorite genes.…”

Section: Discussion and Future Prospectsmentioning

confidence: 99%

RedoxiBase: A database for ROS homeostasis regulated proteins

Savelli

Webber

et al. 2019

Redox Biology

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We present a new database, specifically devoted to ROS homeostasis regulated proteins. This database replaced our previous database, the PeroxiBase, which was focused only on various peroxidase families. The addition of 20 new protein families related with ROS homeostasis justifies the new name for this more complex and comprehensive database as RedoxiBase. Besides enlarging the focus of the database, new analysis tools and functionalities have been developed and integrated through the web interface, with which the users can now directly access to orthologous sequences and see the chromosomal localization of sequences when available. OrthoMCL tool, completed with a post-treatment process, provides precise predictions of orthologous gene groups for the sequences present in this database. In order to explore and analyse orthogroups results, taxonomic visualization of organisms containing sequence of a specific orthogroup as well as chromosomal distribution of the orthogroup with one or two organisms have been included.

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Section: Discussion and Future Prospectsmentioning

confidence: 99%

RedoxiBase: A database for ROS homeostasis regulated proteins

Savelli

Webber

et al. 2019

Redox Biology

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“…Nonetheless, the biologists who work on less-studied plant species might neither have the bioinformatic skills nor afford the computational resources that are required to integrate large-scale RNA-seq data sets and to construct high-quality networks. Thus, user-friendly online or offline tools have been developed to lower the bar for co-expression-based analysis, such as the Kallisto-based LSTrAP pipeline ( Proost et al., 2017 ), the LSTrAP-Cloud ( Tan et al., 2020 ) and the ExpressWeb ( Savelli et al., 2019 ). Besides, computational methods have been reported to improve the quality of co-expression network identification (NetMiner, Yu et al., 2018 ; PCC-HRR Liesecke et al., 2018 ).…”

Section: The Applications Of the Short-read Bulk Rna-seq In Plant Sci...mentioning

confidence: 99%

Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics

Zeng

Zhang

et al. 2022

Front. Plant Sci.

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RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.

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The internet: recent trends

Mohapatra¹

2020

Information Resources in Toxicology

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ExpressWeb: A Web application for clustering and visualization of expression data

Cited by 3 publications

References 8 publications

RedoxiBase: A database for ROS homeostasis regulated proteins

RedoxiBase: A database for ROS homeostasis regulated proteins

Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics

The internet: recent trends

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