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All of these alterations, with the exception of CCND1, which did not meet our frequency threshold, are also clustered together within the RB1 module identified by network analysis (Figure 3A).
The second nitrogenase-related module identified by Spice contains COG1348 (NifH) and COG3883 (Uncharacterized).
A module identified by SSIM can be extended according to the following procedure.
Module 1 is the largest module identified by our clustering analyses and comprises 178 nodes, 15,720 edges, clustering coefficient of 0.692 and network density of 0.499.
This is also true of the top down-regulated module identified by GiGA (Additional file 2: Figure S4A) which contains several small pathways absent from ambient, but for which there are not individual significance values.
The large number of stromal cells, immune cells and tumor-adjacent normal tissue contributes significantly to gene expression levels, which is reflected by the prominent trans-acting association of a T-cell receptor loci gene expression module identified by the investigators.
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List of coexpression modules identified by MCODE.
This study reveals the evolution of products into designs with smaller part counts, closely matching the modules identified by the conceptual DFA method.
The modules identified by ISA are threshold-dependent.
In comparison with traditional clustering methods, the modules identified by ISA are associated with conditions.
The candidate modules identified by Miso 0,1) are exactly the clusters arising in the dendrogram.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com