In order to get a sense of how the reported results compare with the modules reported by other approaches, we ran the NetsTensor algorithm [ 5] on the same dataset.
However, previous studies support the additive effect of the NF-κB+ISRE module, reporting several genes that were co-regulated by NF-κB and ISRE.
Considering the reasonable number of modules and connection of nodes in our healthy subjects, we mainly displayed the modules of healthy control, non-HE and MHE groups at sparsity = 8%, where our healthy control group had the same number of modules as that reported by Salvador et al. [ 30].
The M.I.N.I. module was validated by comparing depressive symptoms reported by the patients themselves using the M.I.N.I. module with those reported by their psychiatrist assessing the presence of DSM-5 criteria during the clinical interview.
The module was validated by comparing depressive symptoms reported by the patients themselves using the M.I.N.I. module with those evaluated by their psychiatrist using DSM-5 criteria during clinical interviewing.
Then, sequences mapped onto respective genomes are subjected to targeted de novo assembly; these include (i) CS and their paired mates from the CS module; (ii) reads from the RP module; and (iii) RPs with one end mapped in the vicinity (500 bp) of the human regions reported by the RP module.
The Cell cycle, Complement and coagulation cascades, Cytokines and Hematopoietic cell lineage modules identified here were also reported by Rubins et al [ 1] as differentially expressed using gene by gene approaches.
Genotype concordance as reported by the GATK Genotype Concordance module was 0.97 (Table 2).
The image quality reported by the template extraction module only weakly correlated with the genuine comparison scores.
Three of the six modules contain components of core GBM pathways reported by the TCGA consortium [ 1], which examined a subset of the 145 tumors we analyzed.
