GeneCloudOmics: A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis.
OMICS data
RNA-seq
bioinformatics
data analytics
gene expression analysis
microarray
transcriptomics
Journal
Frontiers in bioinformatics
ISSN: 2673-7647
Titre abrégé: Front Bioinform
Pays: Switzerland
ID NLM: 9918227263306676
Informations de publication
Date de publication:
2021
2021
Historique:
received:
07
05
2021
accepted:
14
10
2021
entrez:
28
10
2022
pubmed:
29
10
2022
medline:
29
10
2022
Statut:
epublish
Résumé
Gene expression profiling techniques, such as DNA microarray and RNA-Sequencing, have provided significant impact on our understanding of biological systems. They contribute to almost all aspects of biomedical research, including studying developmental biology, host-parasite relationships, disease progression and drug effects. However, the high-throughput data generations present challenges for many wet experimentalists to analyze and take full advantage of such rich and complex data. Here we present GeneCloudOmics, an easy-to-use web server for high-throughput gene expression analysis that extends the functionality of our previous ABioTrans with several new tools, including protein datasets analysis, and a web interface. GeneCloudOmics allows both microarray and RNA-Seq data analysis with a comprehensive range of data analytics tools in one package that no other current standalone software or web-based tool can do. In total, GeneCloudOmics provides the user access to 23 different data analytical and bioinformatics tasks including reads normalization, scatter plots, linear/non-linear correlations, PCA, clustering (hierarchical, k-means, t-SNE, SOM), differential expression analyses, pathway enrichments, evolutionary analyses, pathological analyses, and protein-protein interaction (PPI) identifications. Furthermore, GeneCloudOmics allows the direct import of gene expression data from the NCBI Gene Expression Omnibus database. The user can perform all tasks rapidly through an intuitive graphical user interface that overcomes the hassle of coding, installing tools/packages/libraries and dealing with operating systems compatibility and version issues, complications that make data analysis tasks challenging for biologists. Thus, GeneCloudOmics is a one-stop open-source tool for gene expression data analysis and visualization. It is freely available at http://combio-sifbi.org/GeneCloudOmics.
Identifiants
pubmed: 36303746
doi: 10.3389/fbinf.2021.693836
pii: 693836
pmc: PMC9581002
doi:
Types de publication
Journal Article
Langues
eng
Pagination
693836Informations de copyright
Copyright © 2021 Helmy, Agrawal, Ali, Soudy, Bui and Selvarajoo.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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