From a total of 751 clusters that presented significant hits in the databases, 33.3% represent proteins involved in various cellular functions.
Using GO term enrichment analysis, we found terms in the clusters that presented significant correlation with whole plant LN conditions (Module 4), LN conditions in leaves (Module 6), and N reduction in leaves (Module 10) and roots (Module 9).
This latter explanation is attractive because we verified that clusters that presented intron retention have more cDNAs than all other genes (for example, ~17% of the intron retaining and 6% of all other clusters, have > 400 cDNAs, χ-test, 1 d.f., P < 10-10, see distribution of cluster sizes in Figure S2 of the Additional file 3: Analysis of gene expression).
During NOx reduction with CH4 over Pd/zeolite catalysts, H/D exchange of methane has been observed, indicating that methane is dissociatively adsorbed on Pd0 clusters that are present in the steady-state of surface oxidation and reduction steps.
Pursuit of repeated sequence elements not necessarily coding for proteins, employing a strategy described in Abouelhoda et al., [28] (see methods), allowed us to define 20 clusters that are present more than once in the CS-505 genome.
On the other hand, when the rewiring rules are restricted to a local neighborhood, each new node cannot always choose the best rewiring to synchronize with a given cluster, and thus may end up with an average frequency different from the synchronized clusters that were present.
Many existing software allow for clusters that are present in less than 50% of the trees.
The Los Angeles study area had two clusters that were present only at a lag time of 20 years.
Based on this, our implementation contains an algorithm that verifies that a computed galled network does indeed contain all clusters that are present in the input.
The conserved genes are defined as gene clusters that are present in all analyzed genomes (please note the difference from the definition of specific genes).
