5. Click the Home icon to return to the overview screen. Click on
the different tabs to explore the ontologies of anatomy and
perturbations (including response in mutants; you will need to
sign up for a free trial for this). The expression of ABI3 is high
in the seed arrays, principally in the embryo and endosperm,
rather than in the seed coat. By genotype, ABI3 is highly
expressed in the pER8:LEC1 overexpression line and repressed
in lec1.1 plants; in contrast, ABI3 has lower expression in the
pif1/pif3/pif4/pif5 quadruple mutant plants. ABA treatments
promote its expression, as does the treatment with Paclobutrazol (a GA inhibitor).
6. We can generate hypotheses from these data: phytochromemediated light signaling and downstream factors regulate ABI3
expression, and LEC1 likely regulates ABI3 expression either
directly or indirectly.
7. Note: Genevisible at https://genevisible.com/search may be
freely used to search the developmental or perturbation compendia Genevestigator has compiled to identify the 20 developmental data sets or conditions where your gene of interest has
the strongest and weakest expression.
3.5 Coexpression
Tools
Coexpression analysis can leverage the large number of gene
expression data sets that have been generated in the past decade
to answer the question “which genes show similar patterns of
expression as my gene of interest, across all samples in a given
database?”. Those that show similar patterns of expression may be
involved in the same biological process as the query gene, after the
“guilt-by-association” paradigm. The use of such analyses is well
covered in a review by Usadel and colleagues [8].
3.5.1 Expression Angler
Expression Angler [30] is a powerful yet easy-to-use tool for identifying coexpressed genes, as measured by the Pearson correlation
coefficient—r, in both a condition-dependent and conditionindependent manner (see Note 12). With it, it is possible to answer
the question of which genes show similar patterns of expression in
9 different compendia—genes with an r-value of greater than
around 0.75 can be considered coexpressed. It is also possible to
use just a subset of the samples within a given data set to perform
the analysis, which we will do below for ABI3. Those genes annotated as “unknown function” or those with vague descriptions may
be involved in the same process as the query gene. .
1. Go to the Bio-Analytic Resource for Plant Biology’s homepage
at http://bar.utoronto.ca and select the Legacy Expression
Angler link (a revamped version of this tool is also available
but it is difficult to do the following with it).
Arabidopsis Bioinformatics
41
the different tabs to explore the ontologies of anatomy and
perturbations (including response in mutants; you will need to
sign up for a free trial for this). The expression of ABI3 is high
in the seed arrays, principally in the embryo and endosperm,
rather than in the seed coat. By genotype, ABI3 is highly
expressed in the pER8:LEC1 overexpression line and repressed
in lec1.1 plants; in contrast, ABI3 has lower expression in the
pif1/pif3/pif4/pif5 quadruple mutant plants. ABA treatments
promote its expression, as does the treatment with Paclobutrazol (a GA inhibitor).
6. We can generate hypotheses from these data: phytochromemediated light signaling and downstream factors regulate ABI3
expression, and LEC1 likely regulates ABI3 expression either
directly or indirectly.
7. Note: Genevisible at https://genevisible.com/search may be
freely used to search the developmental or perturbation compendia Genevestigator has compiled to identify the 20 developmental data sets or conditions where your gene of interest has
the strongest and weakest expression.
3.5 Coexpression
Tools
Coexpression analysis can leverage the large number of gene
expression data sets that have been generated in the past decade
to answer the question “which genes show similar patterns of
expression as my gene of interest, across all samples in a given
database?”. Those that show similar patterns of expression may be
involved in the same biological process as the query gene, after the
“guilt-by-association” paradigm. The use of such analyses is well
covered in a review by Usadel and colleagues [8].
3.5.1 Expression Angler
Expression Angler [30] is a powerful yet easy-to-use tool for identifying coexpressed genes, as measured by the Pearson correlation
coefficient—r, in both a condition-dependent and conditionindependent manner (see Note 12). With it, it is possible to answer
the question of which genes show similar patterns of expression in
9 different compendia—genes with an r-value of greater than
around 0.75 can be considered coexpressed. It is also possible to
use just a subset of the samples within a given data set to perform
the analysis, which we will do below for ABI3. Those genes annotated as “unknown function” or those with vague descriptions may
be involved in the same process as the query gene. .
1. Go to the Bio-Analytic Resource for Plant Biology’s homepage
at http://bar.utoronto.ca and select the Legacy Expression
Angler link (a revamped version of this tool is also available
but it is difficult to do the following with it).
Arabidopsis Bioinformatics
41