6. Click on the small “L”-shaped icon in the Link column for each
coexpressed gene to get the same information described in step
3. One of the most powerful features of ATTED II is the
network visualization of coexpressed genes. This network visually depicts genes connected directly and indirectly to our
query gene by coexpression. We can explore coexpression network neighborhoods by clicking on the gene-names (see
Fig. 8).
7. ATTED II shows that ABI3 is coexpressed with EPR1
(an extensin-like gene) that is involved in seed germination,
but only expressed in the endosperm [34]. AIL5 (AINTEGUMENTA LIKE-5; also called PTL5) appears to be coexpressed
with ABI3 as well. AIL5 encodes a member of the AP2 family
of transcriptional regulators that are involved in cell proliferation activities in many organs [35]. AIL5 mutants are resistant
to ABA. We can therefore hypothesize that ABI3 and AIL5 act
together to control cell proliferation and/or ABA response.
3.5.3 AraNet
AraNet uses machine learning to train networks of correlated genes
from a “gold standard” of reliable Gene Ontology annotations and
pathways from MetaCyc, using the guilt-by-association principle
Fig. 8 Output of an ATTED II query for the ABI3 gene, showing ranked list of coexpressed genes in ATTED II’s
condition independent data set (top panel) and a visualization of the coexpression list in network form (insert)
44
G. Alex Mason et al.
coexpressed gene to get the same information described in step
3. One of the most powerful features of ATTED II is the
network visualization of coexpressed genes. This network visually depicts genes connected directly and indirectly to our
query gene by coexpression. We can explore coexpression network neighborhoods by clicking on the gene-names (see
Fig. 8).
7. ATTED II shows that ABI3 is coexpressed with EPR1
(an extensin-like gene) that is involved in seed germination,
but only expressed in the endosperm [34]. AIL5 (AINTEGUMENTA LIKE-5; also called PTL5) appears to be coexpressed
with ABI3 as well. AIL5 encodes a member of the AP2 family
of transcriptional regulators that are involved in cell proliferation activities in many organs [35]. AIL5 mutants are resistant
to ABA. We can therefore hypothesize that ABI3 and AIL5 act
together to control cell proliferation and/or ABA response.
3.5.3 AraNet
AraNet uses machine learning to train networks of correlated genes
from a “gold standard” of reliable Gene Ontology annotations and
pathways from MetaCyc, using the guilt-by-association principle
Fig. 8 Output of an ATTED II query for the ABI3 gene, showing ranked list of coexpressed genes in ATTED II’s
condition independent data set (top panel) and a visualization of the coexpression list in network form (insert)
44
G. Alex Mason et al.