For example, by incorporating a prior noise-distribution to improve the parameter estimation in the commonly used CAGED model (Cluster Analysis of Gene Expression Dynamic, Wangg et al. achieved more functional and meaningful clusters, as validated by Gene Ontology [ 43].
In the bystander gene response, there was more functional overlap between clusters compared with the radiation gene response (Table 7).
The analysis of gene co-expression network provides powerful searching ability that allowed us to identify more than 400 functional clusters related to SMA.
Generally, both DAVID and GOrilla demonstrated significant enrichment of similar GO terms, with DAVID producing a more succinct set of functional clusters (table 2).
On the other hand, less ω and larger p result in more clusters, so the resulting clusters can identify more functional modules; however, the result contains relatively redundant and low-quality clusters, so a number of resulting clusters cannot precisely match functional modules.
More clearly, the 13 overrepresented functional clusters confirm the main biological processes.
More detailed inspection identified important functional clusters among the neuronally enriched genes (Fig. 5; Supplemental Fig. S3).
10 or more genes are in specific functional clusters that carry out general processes such as DNA and chromosomal replication, cell cycle regulation, transcription, and translation.
In the context of the results of this study, this would imply that white-throated sparrows, with many more functional TAS2Rs in this particular cluster than either the chicken or zebra finch, are likely to be more finely tuned in their perception of bitter compounds that are ligands for the receptors in this cluster compared with the other two species.
The Ugt1 clusters in these two old-world-monkey species contain one more functional variable exon than the human and chimpanzee Ugt1 clusters.
