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We then assessed module synteny between the four strains studied, by aligning conserved modules on linear genomic maps.
To compare the performances of unsigned and signed WGCNA in identifying gene groups that are important for the regulation of the pluripotent state, we defined gene modules in unsigned and signed networks and assessed module function and importance by determining gene ontology terms associated with each module and examining module membership of genes known to play a role in ES cells.
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Moreover, known protein complexes are largely incorporated in the assessed modules.
We measured several GO-based quantities to assess module quality.
While the cross-tabulation based module overlap analysis is a simple and intuitive way of assessing module preservation, it has several limitations.
We ran separate WGCNA analyses for each sex (n = 7 for females and n = 8 for males) to assess module preservation across sex.
To assess module specificity, we compared the performance of each of them in the disease in which they were identified against its performance across all other diseases.
At intake, 13 children were assessed with Module 1 and five children with Module 2. At follow-up, 11 children were assessed with Module 1 and seven children with Module 2. KSPD, Kyoto Scale Psychological Development Test.
All participants were assessed using module 4 of the ADOS on the date of scanning (Lord et al. 2000).
To assist with the categorisation of co-expressed genes and partitioned modules according to their potential function or processes, we assessed the modules for enrichment primarily for GO terms in R (http://www.r-project.org) using the 'gProfileR' package [ 37] to interface g:profiler (http://gprofiler.at.mt.ut.ee/gprofiler/).ee/gprofiler/
It's worth remembering that from next academic year, A-levels will no longer be assessed in modules.
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