average value (not median) when comparing two expression
vectors. Another useful display is the “View formatted data
set,” which shows untransformed expression levels.
5. By mousing over the heatmap, it is possible to find out the
annotation of the genes, which samples they are expressed most
strongly in, and other information. Interestingly, YABBY3,
likely a patterning gene, shows up as being coexpressed with
ABI3, as are several other transcription factors.
3.5.2 ATTED II
ATTED II [32] is a gene coexpression database for finding functional relationships between genes. This tool uses the mutual rank
(MR) of the Pearson’s correlation coefficient [33] to investigate
gene coexpression in Arabidopsis in a condition-independent way
or across five sets of experimental conditions: tissue, abiotic stress,
biotic stress, hormones, and light conditions. ATTED II also offers
analysis of rice coexpression data to provide a comparative view
between both species using putative gene orthologs.
1. Go to http://atted.jp/.
2. On the search menu, click on the arrow(s) on the right-hand
side of the pull-down menu and select the option that best fits
your search (“All words,” “Keyword,” “Gene alias,” “Gene
ID,” or “GO ID”). We will search by “Gene ID,” At3g24650
for ABI3. Click Search after entering it in the box.
3. The output window shows a brief description of the gene of
interest, such as the alias and the function. By clicking the little
“L”-shaped icon in the Locus Page column, ATTED II sends
us to a new window with a lot of information about the gene:
functional annotation, a gene coexpression network, gene
expression levels, and predicted cis elements.
4. For a more extensive analysis of coexpressed genes, go back to
the locus search window and click on “list” of coexpressed
genes. The program will give a list of the top 300 coexpressed
genes (see Note 14).
5. Check “coex in specific conditions” to study coexpression
under different conditions: tissue, abiotic stress, biotic stress,
hormone, and light. We can rank coexpression in each condition by clicking on “sort” in that column’s heading. This
approach would help us to infer the gene’s function in each
category. For instance, the genes that are more closely correlated to ABI3 differ extensively depending on which biological
context we are interested in. This suggests that ABI3 has
multiple functions—both developmentally and in response to
the environment, i.e., if we sort by “tissue,” ABI3 is coexpressed with several seed-associated genes, whereby different
genes show up at the top of the ABI3-coexpressed lists under
hormone treatments or abiotic stress.
Arabidopsis Bioinformatics
43
vectors. Another useful display is the “View formatted data
set,” which shows untransformed expression levels.
5. By mousing over the heatmap, it is possible to find out the
annotation of the genes, which samples they are expressed most
strongly in, and other information. Interestingly, YABBY3,
likely a patterning gene, shows up as being coexpressed with
ABI3, as are several other transcription factors.
3.5.2 ATTED II
ATTED II [32] is a gene coexpression database for finding functional relationships between genes. This tool uses the mutual rank
(MR) of the Pearson’s correlation coefficient [33] to investigate
gene coexpression in Arabidopsis in a condition-independent way
or across five sets of experimental conditions: tissue, abiotic stress,
biotic stress, hormones, and light conditions. ATTED II also offers
analysis of rice coexpression data to provide a comparative view
between both species using putative gene orthologs.
1. Go to http://atted.jp/.
2. On the search menu, click on the arrow(s) on the right-hand
side of the pull-down menu and select the option that best fits
your search (“All words,” “Keyword,” “Gene alias,” “Gene
ID,” or “GO ID”). We will search by “Gene ID,” At3g24650
for ABI3. Click Search after entering it in the box.
3. The output window shows a brief description of the gene of
interest, such as the alias and the function. By clicking the little
“L”-shaped icon in the Locus Page column, ATTED II sends
us to a new window with a lot of information about the gene:
functional annotation, a gene coexpression network, gene
expression levels, and predicted cis elements.
4. For a more extensive analysis of coexpressed genes, go back to
the locus search window and click on “list” of coexpressed
genes. The program will give a list of the top 300 coexpressed
genes (see Note 14).
5. Check “coex in specific conditions” to study coexpression
under different conditions: tissue, abiotic stress, biotic stress,
hormone, and light. We can rank coexpression in each condition by clicking on “sort” in that column’s heading. This
approach would help us to infer the gene’s function in each
category. For instance, the genes that are more closely correlated to ABI3 differ extensively depending on which biological
context we are interested in. This suggests that ABI3 has
multiple functions—both developmentally and in response to
the environment, i.e., if we sort by “tissue,” ABI3 is coexpressed with several seed-associated genes, whereby different
genes show up at the top of the ABI3-coexpressed lists under
hormone treatments or abiotic stress.
Arabidopsis Bioinformatics
43