What does Arabidopsis Coexpression Tool do?

Arabidopsis Coexpression Tool (ACT) is used for the identification of transcriptionally correlated (coexpressed) genes in Arabidopsis thaliana.

How do I cite Arabidopsis Coexpression Tool?

What data are stored and where do they come from?

ACT database mainly contains:

What is the input and output of ACT?

The Gene Name or the Gene Symbol of a gene of interest can be used as input. The output shows the most closely coexpressed genes to the driver gene as a coexpression subtree, as well as their Gene names, Gene Symbols and descriptions. A biological term category can be picked from the drop down menu to perform an Over-representation analysis.

What is the Over-representation analysis?

By selecting one of the available Enrichment Analyses from the drop down menu, ACT will perform a term over-representation analysis for each term in that category that describes the list of the coexpressed genes. The statistical significance (p-value) of the over-representation of each term is based on Hypergeometric Distibution. P-values are adjusted using Benjamini–Hochberg procedure. The Enrichment Summary only outputs terms whose over-representation p-value is below the 0.05 Cut-off.

What are the ThaleMine Gene Annotation, Gene Ontology: Biological Process, Gene Ontology: Cellular Component, Gene Ontology: Molecular Function, Plant Ontology: Plant Anatomy, Plant Ontology: Plant Structure Developmental Stage, WikiPathways, KEGG Pathway, AraCyc, AtRegNet and Pfam lists useful for?

Eleven different sorts of analyses can be performed:

How can I navigate through the lists?

The user can change enrichment analysis by selecting another category. Alternatively, the user can select a different driver gene by clicking on a different probe set (which is composed of the Gene name and the "_at" suffix). The user can also visit external sources that are related to the terms shown on the analysis.

What is the gene list useful for?

The user can download the current tree gene list that can be used for further analyses in external websites. Automatic redirections to the Thalemine list analysis and to the String website are already provided.

How can I navigate through the trees?

Further to the list navigation, the user can choose to see more or less nodes of the subtree. The Newick formatted subtree can also be downloaded. The tree can also be viewed externally in the iTol tree viewer.

What are your contact details?

Contact Dr Ioannis Michalopoulos

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The “ELIXIR-GR: Managing and Analysing Life Sciences Data (MIS: 5002780)” Project is co-financed by Greece and the European Union - European Regional Development Fund