Figure 3: (CAN MATT VERIFY THAT I USED THE FINAL NETWORK?) Summarising
the network by GO term. (A) In order to look for enrichments for pairs
of GO terms that are associated with one another, we counted the
frequency of a certain GO term being upstream of each other GO term. To
determine how likely we were to observe this by chance, we shuffled the
GO terms, but kept the network structure, and calculated a null
distribution from which to calculate a p-value. (B) A heatmap of the
resulting p-values from the procedure in (A), clustered using the
default parameters of hclust. We repeated this twice, once with a
network that contained all the genes and once with a network that
contained genes encoding DNA binding proteins only. This is showing the
table for the latter. It is possible to show this as a network by only
including edges with a p-value below a threshold. We show this for (C)
the network with all genes and (D) the network only containing DNA
binding proteins.
Analysis of network edges that are consistent with TF
binding
data
Next, we found a subset of regulatory associations that is supported
both by our inferred network and by DNA binding data (via DAP-seq
from (O’Malley et al. 2016)). We find that the resulting network forms
eight disconnected sub-networks, as shown in Figure 4A (in
addition to a set of disconnected edges, see Table S5– not
done ).
These include networks involved in temperature response, either via HSFs
(blue) or C-REPEAT/DRE BINDING FACTOR 2 (CBF2) and SHORT VEGETATIVE
PHASE (SVP) (pink). Interestingly, both these subnetworks are
up-regulated in elevated temperatures, although the HSF-driven network
has raised expression in phyAphyBcry1cry2 , while the CBF2/SVP
subnetwork has increased expression in prr5prr7prr9 . Previously,
when we analysed the entire set of DNA binding genes, we had found that
there is an early burst of gene expression that is elevated at
27oC, which was upregulated in phyAphyBcry1cry2to a greater extent than prr5prr7prr9 . Since this cluster of
genes included HSF1A, it may be that this early burst of gene expression
drives the expression of the subnetwork containing HSFB2B, HSP90, and
HSP60. Indeed, we see that this subnetwork experiences reduced
expression in hsf1abcd .
Additionally, we find a subnetwork of genes (orange) that include a
number of genes that can respond to ABA signalling within an hour of
signalling (HB6, HB7, CHX17, HAI1, and ATAF1). To put this result in
context, out of the approximately 30,000 total genes
in Arabidopsis , there are less than 300 genes with significantly
increased expression (FDR<0.001) after 1 hour exposure to ABA
(Song et al. 2016).
Another subnetwork is centred on MYBS2 (brown), which is also known to
increase the sensitivity to ABA (Chen et al. 2016). The HB6/HB7 centred
subnetwork has a number of genes with increased expression inphyAphyBcry1cry2 , while the MYBS2-centred subnetwork is
up-regulated in prr5prr7prr9 . Both of these networks are
up-regulated in elevated temperature.
phyAphyBcry1cry2 and prr5prr7prr9 also have opposite
effects in the network that includes GBF6, BBX31, ERF39, MYB13 and HAT2,
which includes genes involved in biosynthesis and metabolism, as well as
cold tolerance. These genes are up-regulated in prr5prr7prr9, but
downregulated in phyAphyBcry1cry2.