Co-expression for Genotype-Phenotype Function Annotation in Potato Research

Oren Tzfadia

doi:10.1007/978-1-0716-1609-3_12

Co-expression for Genotype-Phenotype Function Annotation in Potato Research

Methods Mol Biol. 2021:2354:261-272. doi: 10.1007/978-1-0716-1609-3_12.

Author

Oren Tzfadia¹

Affiliation

¹ Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. otzfadia@itg.be.

PMID: 34448164
DOI: 10.1007/978-1-0716-1609-3_12

Abstract

Here we will show a recipe for running the online version of CoExpNetViz, which is available as a Cytoscape plug-in, and as a web tool. After choosing bait genes and transcriptome datasets in the Cytoscape plug-in, the analysis is run and the resulting network is displayed immediately. Using the web tool, the user can download the Cytoscape files and import them manually into the program.The easiest way to calculate correlations for your data is to use graphical interface online version of CoExpNetViz for the comparative co-expression construction; see http://bioinformatics.psb.ugent.be/webtools/coexpr/index.php .By providing a user-friendly web interface, CoExpNetViz makes comparative transcriptomics analysis accessible to plant researchers without specialized bioinformatics knowledge or programming skills.

Keywords: Bioinformatics; Co-expression; Network analysis; Transcriptomics.

MeSH terms

Computational Biology
Genotype
Phenotype
Software*
Solanum tuberosum* / genetics