instance, clicking on the 9-cis-epoxycarotenoid dioxygenase
will give all interactions in which this enzyme could be involved
in, as well as the enzymatic reactions of all closely related
homologs.
6. To get detailed information on the gene, double-click on the
gene name. For instance, ABA4 (At1g67080) encodes a neoxanthin synthase involved in the conversion of violaxathin into
trans-neoxanthin, which is an early step in ABA biosynthesis.
We can expect that mutants in ABA4 have reduced levels of
ABA, hence the expression of ABI3 will be reduced too since it
is ABA-responsive [27]. Transcriptome analysis of aba4
mutants would be useful to study the plant’s behavior in the
absence of ABA to determine any correlation with loss of ABI3
function.
In Subheading 3.4.4 (Genevestigator) we determined that
ABI3 was upregulated in LEC1 overexpression plants (pER8LEC1). We will use the list of genes upregulated in LEX1-OX
plants [10] to predict metabolic pathways that LEC1 overexpression modulated with the OMICs Viewer tool of the AraCyC database. Download the file here (see Note 1). These genes may act with
ABI3 to influence plant form or function.
1. Go to http://pmn.plantcyc.org/overviewsWeb/celOv.shtml
(you can access this from the Metabolism tab at the top of the
AraCyc page, too).
2. In the right part of the window, the OMICs Viewer presents
various operations we can perform with it. Click on the
“Upload Data from File” option. The file must be in
tab-delimited text format and the first column must be the
Fig. 17 Overview of ABA biosynthesis in AraCyc as resulting from a query with “abscisic acid biosynthesis.”
Arabidopsis Bioinformatics
61
will give all interactions in which this enzyme could be involved
in, as well as the enzymatic reactions of all closely related
homologs.
6. To get detailed information on the gene, double-click on the
gene name. For instance, ABA4 (At1g67080) encodes a neoxanthin synthase involved in the conversion of violaxathin into
trans-neoxanthin, which is an early step in ABA biosynthesis.
We can expect that mutants in ABA4 have reduced levels of
ABA, hence the expression of ABI3 will be reduced too since it
is ABA-responsive [27]. Transcriptome analysis of aba4
mutants would be useful to study the plant’s behavior in the
absence of ABA to determine any correlation with loss of ABI3
function.
In Subheading 3.4.4 (Genevestigator) we determined that
ABI3 was upregulated in LEC1 overexpression plants (pER8LEC1). We will use the list of genes upregulated in LEX1-OX
plants [10] to predict metabolic pathways that LEC1 overexpression modulated with the OMICs Viewer tool of the AraCyC database. Download the file here (see Note 1). These genes may act with
ABI3 to influence plant form or function.
1. Go to http://pmn.plantcyc.org/overviewsWeb/celOv.shtml
(you can access this from the Metabolism tab at the top of the
AraCyc page, too).
2. In the right part of the window, the OMICs Viewer presents
various operations we can perform with it. Click on the
“Upload Data from File” option. The file must be in
tab-delimited text format and the first column must be the
Fig. 17 Overview of ABA biosynthesis in AraCyc as resulting from a query with “abscisic acid biosynthesis.”
Arabidopsis Bioinformatics
61