mapping according to the data. If the data contain AGI IDs,
use Ath_AGI_TAIR (if they contain Affymetrix IDs, use
Ath_AFFY_TAIR). For LEC1OX genes, click on the data file
uploaded in step 3.
5. MapMan shows a representation of the pathways and genes
showing altered regulation (see Fig. 19). Each gene is symbolized by a square and expression is color encoded (by default
red denotes downregulated, blue denotes upregulated). As we
are looking at over-expressed genes in the LEC1OX, we only
see blue colors. We can see that LEC1 overexpression promotes
the expression of transcription factors and genes involved in
protein modification and degradation. Looking at hormone
pathways, we can see that LEC1 promotes the expression of
genes involved in auxin, brassinosteroid, and gibberellin
metabolism. Below the pathway representation, there is information about the statistical enrichment (using the Wilcoxon
rank sum test) performed in MapMan. Mouse over gene
squares to see information about gene function, name, and
expression value. More information about how to use MapMan
with experimental data is provided in an online tutorial on the
MapMan site.
Fig. 19 Output of a MapMan pathway analysis using genes upregulated in LEC1OX plants (see text)
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G. Alex Mason et al.
use Ath_AGI_TAIR (if they contain Affymetrix IDs, use
Ath_AFFY_TAIR). For LEC1OX genes, click on the data file
uploaded in step 3.
5. MapMan shows a representation of the pathways and genes
showing altered regulation (see Fig. 19). Each gene is symbolized by a square and expression is color encoded (by default
red denotes downregulated, blue denotes upregulated). As we
are looking at over-expressed genes in the LEC1OX, we only
see blue colors. We can see that LEC1 overexpression promotes
the expression of transcription factors and genes involved in
protein modification and degradation. Looking at hormone
pathways, we can see that LEC1 promotes the expression of
genes involved in auxin, brassinosteroid, and gibberellin
metabolism. Below the pathway representation, there is information about the statistical enrichment (using the Wilcoxon
rank sum test) performed in MapMan. Mouse over gene
squares to see information about gene function, name, and
expression value. More information about how to use MapMan
with experimental data is provided in an online tutorial on the
MapMan site.
Fig. 19 Output of a MapMan pathway analysis using genes upregulated in LEC1OX plants (see text)
64
G. Alex Mason et al.