(This might need to be moved to the methods or the beginning of
the next section)
TODO: get clusters from consensus clustering and see if there
is enrichment in GO terms
Figure S3: Consensus clustering (DONE)
Figure S4: Expression of genes that come from consensus clustering.
(DONE)
An early morning gene regulatory
network
Given this set of genes, we wished to identify possible regulatory links
by inferring a gene regulatory network. Because genes change their
expression rapidly at dawn, it is likely that there is a time delay
between the time the gene is expressed and the time the protein is
expressed. For this reason, we applied a time delay network inference
method called dynGenie3. This analysis predicted a dense hairball
network (Figure S5– not done ) that had qualities of a
scale-free network (Figure S6 ). Although there was some
spatial localisation by time of peak expression (Figure S7 ) and
GO term (Figure S8 ), it is hard to interpret such a dense
network.
To be able to interpret this dense network, we wished to determine
whether genes associated with certain GO terms were found upstream or
downstream of genes with other GO terms (Figure 3A ). We
compared the observed frequency of regulatory relationships between
genes with certain GO terms in our predicted network with the expected
frequencies, calculated by repeatedly shuffling the GO terms
(Figure 3A ). This would help us learn how pathways related to
light, circadian, and temperature interact with one another. Within our
inferred network, only genes that are labelled ‘DNA binding’ can
regulate other genes, so this GO term was not included in the analysis
unless it was the only GO term associated with a given gene. In the
network that only includes DNA binding genes, we observe that circadian,
light, phosphorylation and signalling genes tend to be upstream
regulators, while temperature and growth tend to be downstream
(Figure 3B ). Interestingly, we see that abscisic acid (ABA)
genes tend to be upstream of cold, water, photosynthesis and
biosynthesis genes– this matches well with the known role of ABA
signalling (Daszkowska-Golec 2016).
It is also possible to depict these results as a network that only
includes edges where there is a p-value<0.05. We developed
these networks for all genes (Figure 3C ) and for DNA binding
genes (Figure 3D ). hormone-related GO terms are more
well-connected in the network that includes all genes than the network
that only includes DNA binding proteins, suggesting that hormone-related
DNA binding genes may regulate genes that do not have DNA binding
capacity (Figure 3C ). Within the DNA binding-only network, the
circadian genes seem to interact with light and temperature genes, but
there is no enrichment between light and temperature directly
(Figure 3D ) .