2. In the first section for selecting the analysis tool, select “Singular Enrichment Analysis (SEA).”
3. Select the species (the default is Arabidopsis thaliana).
4. Paste in the Query list as AGI IDs, gene aliases (e.g., ABI3),
GenBank IDs, etc. A large number of different identifiers are
supported.
5. Choose a reference—if the list comes from a microarray experiment, then choose the appropriate microarray platform, otherwise if the list comes from an experiment where it is possible to
identify any of the AGI IDs present in the TAIR genome
annotation (such as the case with a proteomics experiment or
an mRNA-seq experiment) then choose the “Arabidopsis
genome locus (TAIR)” option—this aspect is a nice feature of
AgriGO. In this example, we will submit the top 50 genes
coexpressed with ABI3 in the AtGenExpress Tissue Set as
discussed in Subheading 3.5.1, step 2 (see Supplementary
Table S1). As the data used to obtain the coexpressed genes
come from the Affymetrix ATH1 platform, we use this platform as our reference (GPL198).
6. Under “Advanced Options—optional” one can select one of
three methods for statistical enrichment (Hypergeometric distribution, Fisher, or Chi-square) as well as one of seven multiple hypothesis testing correction methods. We recommend the
use of the Yekutieli method and Fisher’s exact distribution (the
defaults).
7. In the output, a table of enriched GO categories for our list of
50 genes is displayed showing that four GO Biological Process
terms (lipid localization, response to abscisic acid stimulus,
macromolecule localization, post-embryonic development)
and two GO Molecular Function terms (nutrient reservoir
activity, lipid binding) are significantly enriched. Examining
these, they seem to “make sense” in the context of the later
stages of seed development, when ABI3 and these genes are
expressed, insofar as this is the time when lipid reserves are
being accumulated and the seed begins to desiccate. There is
also the possibility of creating “Graphical Results” or a “GO
Flash Chart.” If we click on the Generate Image button, the
following output is generated for enriched Biological Processes
(see Fig. 14).
3.7.2 AmiGO
AmiGO [53] provides a generic interface for computing GO term
enrichments for all of the species annotated by the GO
Consortium.
1. Go to http://amigo.geneontology.org/rte to access the
Advanced Options section of the Panther DB enrichment tool.
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G. Alex Mason et al.
3. Select the species (the default is Arabidopsis thaliana).
4. Paste in the Query list as AGI IDs, gene aliases (e.g., ABI3),
GenBank IDs, etc. A large number of different identifiers are
supported.
5. Choose a reference—if the list comes from a microarray experiment, then choose the appropriate microarray platform, otherwise if the list comes from an experiment where it is possible to
identify any of the AGI IDs present in the TAIR genome
annotation (such as the case with a proteomics experiment or
an mRNA-seq experiment) then choose the “Arabidopsis
genome locus (TAIR)” option—this aspect is a nice feature of
AgriGO. In this example, we will submit the top 50 genes
coexpressed with ABI3 in the AtGenExpress Tissue Set as
discussed in Subheading 3.5.1, step 2 (see Supplementary
Table S1). As the data used to obtain the coexpressed genes
come from the Affymetrix ATH1 platform, we use this platform as our reference (GPL198).
6. Under “Advanced Options—optional” one can select one of
three methods for statistical enrichment (Hypergeometric distribution, Fisher, or Chi-square) as well as one of seven multiple hypothesis testing correction methods. We recommend the
use of the Yekutieli method and Fisher’s exact distribution (the
defaults).
7. In the output, a table of enriched GO categories for our list of
50 genes is displayed showing that four GO Biological Process
terms (lipid localization, response to abscisic acid stimulus,
macromolecule localization, post-embryonic development)
and two GO Molecular Function terms (nutrient reservoir
activity, lipid binding) are significantly enriched. Examining
these, they seem to “make sense” in the context of the later
stages of seed development, when ABI3 and these genes are
expressed, insofar as this is the time when lipid reserves are
being accumulated and the seed begins to desiccate. There is
also the possibility of creating “Graphical Results” or a “GO
Flash Chart.” If we click on the Generate Image button, the
following output is generated for enriched Biological Processes
(see Fig. 14).
3.7.2 AmiGO
AmiGO [53] provides a generic interface for computing GO term
enrichments for all of the species annotated by the GO
Consortium.
1. Go to http://amigo.geneontology.org/rte to access the
Advanced Options section of the Panther DB enrichment tool.
56
G. Alex Mason et al.