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?
If you used ACT, please cite:
- Zogopoulos, V.L., Saxami, G., Malatras, A., Angelopoulou, A., Jen, C.H., Duddy, W.J., Daras, G., Hatzopoulos, P., Westhead, D.R., and Michalopoulos, I. (2021). ACT: A tool for gene coexpression analysis in
Arabidopsis thaliana. iScience 24, 102848.
- Zogopoulos, V.L., Malatras, A., and Michalopoulos, I. (2022). Gene coexpression analysis in Arabidopsis thaliana based on public microarray data. STAR Protoc 3, 101208.
Older publications:
- Manfield, I.W., Jen, C.H., Pinney, J.W., Michalopoulos, I., Bradford,
J.R., Gilmartin, P.M., and Westhead, D.R. (2006). Arabidopsis
Co-expression Tool (ACT): web server tools for microarray-based gene
expression analysis. Nucleic Acids Res 34, W504-9.
- Jen, C.H., Manfield, I.W., Michalopoulos, I., Pinney, J.W., Willats,
W.G., Gilmartin, P.M., and Westhead, D.R. (2006). The Arabidopsis
co-expression tool (ACT): a WWW-based tool and database for
microarray-based gene expression analysis. Plant J 46,336-348.
Further reading on coexpression analysis:
- Zogopoulos, V.L., Saxami, G., Malatras, A., Papadopoulos, K., Tsotra, I., Iconomidou, V.A., and Michalopoulos, I. (2022). Approaches in Gene Coexpression Analysis in Eukaryotes. Biology 11, 1019.
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:
- ThaleMine Gene Annotation: This is the default output of the tool. A
description of each gene is shown. There is no Over-representation
analysis at this stage.
- Biological Process: Biological Process is one of the Gene Ontology
aspects. The Biological Process GO Terms for each gene is shown.
Over-representation analysis shows the most over-represented GO Terms of
the collection of GO Terms. This analysis is useful when a repeated term
can imply the biological process the gene is likely to participate in.
- Molecular Function: Molecular Function is one of the Gene Ontology
aspects. The Molecular Function GO Terms for each gene is shown.
Over-representation analysis shows the most over-represented GO Terms of
the collection of GO Terms. This analysis is useful when a repeated term
can imply the molecular function the gene is likely to have.
- Cellular Component: Cellular Component is one of the Gene Ontology
aspects. The Cellular Component GO Terms for each gene is shown.
Over-representation analysis shows the most over-represented GO Terms of
the collection of GO Terms. This analysis is useful when a repeated term
can imply the cellular component the gene is likely to be part of.
- Plant Anatomy: Plant Anatomy is one of the Plant Ontology aspects. The
Plant Anatomy PO Terms for each gene is shown. Over-representation
analysis shows the most over-represented PO Terms of the collection of
PO Terms. This analysis is useful when a repeated term can imply the
plant anatomical entity the gene is likely to be expressed in.
- Plant Structure Developmental Stage: Plant Structure Developmental
Stage is one of the Plant Ontology aspects. The Plant Structure
Developmental Stage PO Terms for each gene is shown. Over-representation
analysis shows the most over-represented PO Terms of the collection of
PO Terms. This analysis is useful when a repeated term can imply the
plant structure and developmental stage the gene set is likely to be
expressed in.
- WikiPathways: The WikiPathways terms and their descriptions for each
gene is shown. Over-representation analysis shows the most
over-represented WikiPathways terms. This analysis is useful when a
repeated term can imply the pathway the gene is likely to participate
in.
- KEGG Pathway: The KEGG Pathway terms and their descriptions for each
gene is shown. Over-representation analysis shows the most
over-represented KEGG terms. This analysis is useful when a repeated
term can imply the pathway the gene is likely to participate in.
- AraCyc: The AraCyc Plant Metabolic Pathway terms and their
descriptions for each gene is shown. Over-representation analysis shows
the most over-represented AraCyc terms. This analysis is useful when a
repeated term can imply the plant metabolic pathway the gene is likely
to participate in.
- AtRegNet: The ThaleMine names and the descriptions of the
Transcription Factors that bind to the regulatory sequences of each gene
is shown. Over-representation analysis shows the most over-represented
Transcription Factors. This analysis is useful when a repeated term can
imply the list of transcription factors which drive coexpression.
- Plant Cistrome Database: The ThaleMine names and the descriptions of the
Transcription Factors that bind to the regulatory sequences of each gene
is shown. Over-representation analysis shows the most over-represented
Transcription Factors. This analysis is useful when a repeated term can
imply the list of transcription factors which drive coexpression and is different from AtRegNet as it contains more recent data from non-amplified and amplified DAP-seq experiments and more Transcription Factors.
- Pfam: The Pfam terms and their descriptions for each gene is shown.
Over-representation analysis shows the most over-represented Pfam terms
of the collection of Pfam terms. This analysis is useful when a repeated
term can imply the protein family the gene is likely to belong to.
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.
Is there an API available?
ACT coexpression results are available through a public JSON-based API endpoint which is keyed on gene AGI code, node number and, optionally, enrichment category. For example: https://www.michalopoulos.net/act/api/AT2G36620/5/bp provides the results of Gene Ontology: Biological Process enrichment analysis for the coexpression subtree of 5 ancestral nodes for AT2G36620 driver gene. Instructions and an API parser are available.
What are your contact details?
Contact Dr Ioannis Michalopoulos
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