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As protein-protein interaction networks allow identification of functionally associated proteins or important functional clusters [ 9, 10], NeuroGeM visualizes the protein interaction sub-network around a queried gene; each protein node in the network is color-coded according to the available experimental results deposited in NeuroGeM.
More detailed inspection identified important functional clusters among the neuronally enriched genes (Fig. 5; Supplemental Fig. S3).
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If clustering is an important functional feature for TFBS redundancy in embryonic enhancers of the BX-C, then one prediction is that there should be a greater likelihood of finding two binding sites for a particular TF in close proximity to each other in a defined enhancer when compared with the complex as a whole.
To investigate whether some important functional elements were enriched in the boundaries between adjacent clusters in a cell-type-specific manner, we classified the boundaries in the GM06990 cell line into two types: common boundaries (those that were also cluster boundaries in K562 cell line) and GM-specific boundaries (those within clusters or with the minus state in K562).
The CpG genomic maps of specific CpG deserts that had the DMR confirmed with bisulfite mass spectrometry suggested the small clusters of CpG may be an important functional part of the CpG desert.
Functional clusters for sleep genes.
Functional clusters for wake genes.
Clustering of yeast genes on the basis of their similarities in expression patterns resulted in groups of genes sharing important functional similarities [ 11, 13].
Subsequent clustering identified at least three different functional clusters.
Figure 4 shows three such functional clusters.
We clustered these 84 genes by their functional annotations and identified 8 partially overlapping functional clusters.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com