background are GO Cellular Component terms (this shading
scheme does not apply for MapMan terms).
5. In the Overview section, categories that are overrepresented
relative to the total number of instances of the term in the
overall GO or MapMan database (see Note 20) are bolded.
The relative enrichment is shown on the left, while the absolute
number of counts in a given category is on the right. The color
scheme for the categories is also used in the chart section and
for the bar code in the table section. In the case of a list of the
top 50 genes coexpressed with ABI3 in the Developmental
Map, the Developmental Processes and Transport categories
are overrepresented as might be expected for the number of
genes in this list involved in the process of dormancy as seeds
mature, and in transporting lipids to provide reserves for the
seed when it germinates. These categories are also seen with
AgriGO.
6. The Chart section shows the overrepresented categories relative to the frequency in the overall Arabidopsis genome or in
terms of absolute counts on the left and right side, respectively.
7. The table sections shows details for every single gene in the
input list. A bar code system using the same color scheme as in
the other two sections show that in many cases a given gene
falls into several GO categories. Genes are group by category,
Fig. 16 Output of Classification SuperViewer for a list of the top 50 ABI3-coexpressed genes from a query of
the BAR’s Expression Angler tool in the AtGenExpress Tissue Set compendium (Supplementary Table S1).
Output values may differ slightly due to database updates
Arabidopsis Bioinformatics
59
scheme does not apply for MapMan terms).
5. In the Overview section, categories that are overrepresented
relative to the total number of instances of the term in the
overall GO or MapMan database (see Note 20) are bolded.
The relative enrichment is shown on the left, while the absolute
number of counts in a given category is on the right. The color
scheme for the categories is also used in the chart section and
for the bar code in the table section. In the case of a list of the
top 50 genes coexpressed with ABI3 in the Developmental
Map, the Developmental Processes and Transport categories
are overrepresented as might be expected for the number of
genes in this list involved in the process of dormancy as seeds
mature, and in transporting lipids to provide reserves for the
seed when it germinates. These categories are also seen with
AgriGO.
6. The Chart section shows the overrepresented categories relative to the frequency in the overall Arabidopsis genome or in
terms of absolute counts on the left and right side, respectively.
7. The table sections shows details for every single gene in the
input list. A bar code system using the same color scheme as in
the other two sections show that in many cases a given gene
falls into several GO categories. Genes are group by category,
Fig. 16 Output of Classification SuperViewer for a list of the top 50 ABI3-coexpressed genes from a query of
the BAR’s Expression Angler tool in the AtGenExpress Tissue Set compendium (Supplementary Table S1).
Output values may differ slightly due to database updates
Arabidopsis Bioinformatics
59