2. Paste your gene identifiers into the “Gene IDs” box. Using
Genevestigator, we have shown that ABI3 expression depends
on the presence of LEC1.To better understand this ABI3LEC1 relationship, we will use in this instance genes whose
steady-state transcript level is increased in LEC1 overexpressor
(OX) plants from [10], found in Supplemental Table S1 of that
article—a text file of these data can be downloaded here (see
Note 1)—open it with Excel and copy the AGI IDs in the first
column. This will allow us to determine biological functions
associated with genes that are also overexpressed and likely
downstream of LEC1. Select A. thaliana as the “Species,”
and then submit the query. Click “Submit” (use the Bonferroni
correction option). The partial output for this gene list is
shown in Fig. 15.
3. Forty-five genes from the genes upregulated in LEC1OX
plants are grouped into “lipid metabolic process,” with a pvalue of 8.2e-09 (829 genes in the Arabidopsis genome are
associated with this term, meaning an enrichment in our list of
~3.4-fold over the genome-wide background frequency) (see
Note 18). LEC1 is associated to this term, but it is also associated with other several different terms, such as embryo development and others. These analyses indicate that LEC1 is
sufficient to regulate lipid metabolism, as was observed for
ABI3 coexpressed genes, and supports that LEC1 likely regulates a module of genes, including ABI3, that may coordinate
some aspect of lipid metabolism during seed germination.
Fig. 14 Graphical output from AgriGO for the top 50 ABI3-coexpressed genes in the AtGenExpress Tissue Set
from Supplementary Table S1. The GO Biological Process term “Lipid localization” (red) is most significantly
enriched among these genes
Arabidopsis Bioinformatics
57
Genevestigator, we have shown that ABI3 expression depends
on the presence of LEC1.To better understand this ABI3LEC1 relationship, we will use in this instance genes whose
steady-state transcript level is increased in LEC1 overexpressor
(OX) plants from [10], found in Supplemental Table S1 of that
article—a text file of these data can be downloaded here (see
Note 1)—open it with Excel and copy the AGI IDs in the first
column. This will allow us to determine biological functions
associated with genes that are also overexpressed and likely
downstream of LEC1. Select A. thaliana as the “Species,”
and then submit the query. Click “Submit” (use the Bonferroni
correction option). The partial output for this gene list is
shown in Fig. 15.
3. Forty-five genes from the genes upregulated in LEC1OX
plants are grouped into “lipid metabolic process,” with a pvalue of 8.2e-09 (829 genes in the Arabidopsis genome are
associated with this term, meaning an enrichment in our list of
~3.4-fold over the genome-wide background frequency) (see
Note 18). LEC1 is associated to this term, but it is also associated with other several different terms, such as embryo development and others. These analyses indicate that LEC1 is
sufficient to regulate lipid metabolism, as was observed for
ABI3 coexpressed genes, and supports that LEC1 likely regulates a module of genes, including ABI3, that may coordinate
some aspect of lipid metabolism during seed germination.
Fig. 14 Graphical output from AgriGO for the top 50 ABI3-coexpressed genes in the AtGenExpress Tissue Set
from Supplementary Table S1. The GO Biological Process term “Lipid localization” (red) is most significantly
enriched among these genes
Arabidopsis Bioinformatics
57