Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

Vasileios L Zogopoulos; Apostolos Malatras; Ioannis Michalopoulos

doi:10.1016/j.xpro.2022.101208

Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

STAR Protoc. 2022 Feb 26;3(1):101208. doi: 10.1016/j.xpro.2022.101208. eCollection 2022 Mar 18.

Authors

Vasileios L Zogopoulos¹, Apostolos Malatras², Ioannis Michalopoulos¹

Affiliations

¹ Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
² biobank.cy Center of Excellence in Biobanking and Biomedical Research, University of Cyprus, 2029 Nicosia, Cyprus.

Abstract

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).

Keywords: Bioinformatics; Genomics; Model Organisms; Plant sciences; Systems biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Arabidopsis Proteins* / genetics
Arabidopsis* / genetics
Gene Expression Profiling / methods
Genetic Testing
Oligonucleotide Array Sequence Analysis / methods

Substances

Arabidopsis Proteins