Gene coexpression analysis in Arabidopsis thaliana based on public microarray data
Summary: Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpress...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722000880 |
| _version_ | 1818774564902010880 |
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| author | Vasileios L. Zogopoulos Apostolos Malatras Ioannis Michalopoulos |
| author_facet | Vasileios L. Zogopoulos Apostolos Malatras Ioannis Michalopoulos |
| author_sort | Vasileios L. Zogopoulos |
| collection | DOAJ |
| description | Summary: Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach.For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021). |
| first_indexed | 2024-12-18T10:43:09Z |
| format | Article |
| id | doaj.art-ea80570600f74b9fb9934ce37d84b1ab |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-12-18T10:43:09Z |
| publishDate | 2022-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-ea80570600f74b9fb9934ce37d84b1ab2022-12-21T21:10:36ZengElsevierSTAR Protocols2666-16672022-03-0131101208Gene coexpression analysis in Arabidopsis thaliana based on public microarray dataVasileios L. Zogopoulos0Apostolos Malatras1Ioannis Michalopoulos2Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greecebiobank.cy Center of Excellence in Biobanking and Biomedical Research, University of Cyprus, 2029 Nicosia, CyprusCentre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; Corresponding authorSummary: Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach.For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021).http://www.sciencedirect.com/science/article/pii/S2666166722000880BioinformaticsGenomicsModel OrganismsPlant sciencesSystems biology |
| spellingShingle | Vasileios L. Zogopoulos Apostolos Malatras Ioannis Michalopoulos Gene coexpression analysis in Arabidopsis thaliana based on public microarray data STAR Protocols Bioinformatics Genomics Model Organisms Plant sciences Systems biology |
| title | Gene coexpression analysis in Arabidopsis thaliana based on public microarray data |
| title_full | Gene coexpression analysis in Arabidopsis thaliana based on public microarray data |
| title_fullStr | Gene coexpression analysis in Arabidopsis thaliana based on public microarray data |
| title_full_unstemmed | Gene coexpression analysis in Arabidopsis thaliana based on public microarray data |
| title_short | Gene coexpression analysis in Arabidopsis thaliana based on public microarray data |
| title_sort | gene coexpression analysis in arabidopsis thaliana based on public microarray data |
| topic | Bioinformatics Genomics Model Organisms Plant sciences Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722000880 |
| work_keys_str_mv | AT vasileioslzogopoulos genecoexpressionanalysisinarabidopsisthalianabasedonpublicmicroarraydata AT apostolosmalatras genecoexpressionanalysisinarabidopsisthalianabasedonpublicmicroarraydata AT ioannismichalopoulos genecoexpressionanalysisinarabidopsisthalianabasedonpublicmicroarraydata |