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Modules detected by biclustering methods can therefore be easier to interpret compared with those of decomposition methods, as the exact origin of the local co-expression is better defined.
To identify functional themes, we next clustered all of the stemness-on and –off modules detected by S-MAP according to their patterns across the expression compendium (Figure 5A).
The simple comparison of modules detected by us and MCODE demonstrates that the integration of gene expression and protein interaction indeed helps to detect modules related to pathogenesis, where MCODE only exploits protein interaction information.
Seldom were known domain subdivisions within these modules detected by the rules we applied.
We selected modules detected by SA algorithm for similarity analysis and functional classification.
Enrichment for differentially expressed genes, functional categories, and cell type-specific markers in coexpressed gene modules detected by WGCNA.
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The filtered GO terms were associated for each node in each conserved module detected by NetworkBLAST.
Whenever a co-module detected by the PPA contained one of these four CNS organs (e.g., cerebral cortex and olfactory bulb, Figure 3C), the genes from that co-module were also expressed in the three other CNS organs, although sometimes just below the threshold level that PPA used to add the organ into co-modules (see Methods).
We have shown that the modules detected were established by coupling different symmetry elements and decoupling even a single element into different modules.
For the giant component of TMSN, 42 DNA methylation specific modules were detected by removing the modules only containing 2 elements (see Methods for details).
A laser pumps the first nonlinear crystal to generate time correlated SPDC MIR photon-pairs that are spectrally translated into the visible spectrum by two up-converter modules and detected by two Si SPADs.
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