ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/10/10/1026 |
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| author | Gleb E. Gavrish Dmitry V. Chistyakov Marina G. Sergeeva |
| author_facet | Gleb E. Gavrish Dmitry V. Chistyakov Marina G. Sergeeva |
| author_sort | Gleb E. Gavrish |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T06:43:48Z |
| format | Article |
| id | doaj.art-d0190444de534c82be69e4c9c9bd2d4a |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T06:43:48Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-d0190444de534c82be69e4c9c9bd2d4a2023-11-22T17:28:38ZengMDPI AGBiology2079-77372021-10-011010102610.3390/biology10101026ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpressGleb E. Gavrish0Dmitry V. Chistyakov1Marina G. Sergeeva2Faculty of Bioengineering and Bioinformatics, Moscow Lomonosov State University, 119234 Moscow, RussiaBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, RussiaBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, RussiaConduct 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.https://www.mdpi.com/2079-7737/10/10/1026GEOArrayExpresspolarizationsystematics searchgene expressionbioinformatic tool |
| spellingShingle | Gleb E. Gavrish Dmitry V. Chistyakov Marina G. Sergeeva ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress Biology GEO ArrayExpress polarization systematics search gene expression bioinformatic tool |
| title | ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress |
| title_full | ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress |
| title_fullStr | ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress |
| title_full_unstemmed | ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress |
| title_short | ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress |
| title_sort | argeos a new bioinformatic tool for detailed systematics search in geo and arrayexpress |
| topic | GEO ArrayExpress polarization systematics search gene expression bioinformatic tool |
| url | https://www.mdpi.com/2079-7737/10/10/1026 |
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