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Article

ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress

1
Faculty of Bioengineering and Bioinformatics, Moscow Lomonosov State University, 119234 Moscow, Russia
2
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
*
Author to whom correspondence should be addressed.
Academic Editors: Ioannis Michalopoulos and Apostolos Malatras
Biology 2021, 10(10), 1026; https://doi.org/10.3390/biology10101026
Received: 20 August 2021 / Revised: 27 September 2021 / Accepted: 4 October 2021 / Published: 11 October 2021
(This article belongs to the Special Issue Differential Gene Expression and Coexpression)
A systematic search for datasets of transcriptome data is a hefty task. Therefore, we developed the ARGEOS web tool, which simplifies the search and selection of datasets from various public databases. In addition, the service carries out an advanced analysis of a dataset, including collecting detailed protocols, information on the number of datasets, and providing additional reference information. An example of a cell polarization study exemplifies the effectiveness of the tool.
Conduct a reanalysis of transcriptome data for studying intracellular signaling or solving other experimental problems is becoming increasingly popular. Gene expression data are archived as microarray or RNA-seq datasets mainly in two public databases: Gene Expression Omnibus (GEO) and ArrayExpress (AE). These databases were not initially intended to systematically search datasets, making it challenging to conduct a secondary study. Therefore, we have created the ARGEOS service, which has the following advantages that facilitate the search: (1) Users can simultaneously send several requests that are supposed to be used for systematic searches, and it is possible to correct the requests; (2) advanced analysis of information about the dataset is available. The service collects detailed protocols, information on the number of datasets, analyzes the availability of raw data, and provides other reference information. All this contributes to both rapid data analysis with the search for the most relevant datasets and to the systematic search with detailed analysis of the information of the datasets. The efficiency of the service is shown in the example of analyzing transcriptome data of activated (polarized) cells. We have performed a systematic search of studies of cell polarization (when cells are exposed to different immune stimuli). The web interface for ARGEOS is user-friendly and straightforward. It can be used by a person who is not familiar with database searching. View Full-Text
Keywords: GEO; ArrayExpress; polarization; systematics search; gene expression; bioinformatic tool; transcriptome GEO; ArrayExpress; polarization; systematics search; gene expression; bioinformatic tool; transcriptome
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MDPI and ACS Style

Gavrish, G.E.; Chistyakov, D.V.; Sergeeva, M.G. ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress. Biology 2021, 10, 1026. https://doi.org/10.3390/biology10101026

AMA Style

Gavrish GE, Chistyakov DV, Sergeeva MG. ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress. Biology. 2021; 10(10):1026. https://doi.org/10.3390/biology10101026

Chicago/Turabian Style

Gavrish, Gleb E., Dmitry V. Chistyakov, and Marina G. Sergeeva. 2021. "ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress" Biology 10, no. 10: 1026. https://doi.org/10.3390/biology10101026

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