Finally, we evaluated the histomorphology of tumors from the five subtypes, comparing the epithelial, immune, and stromal components (Supplementary Fig.2f). In general, S1 and S2 tumors had prominent papillary arrangement; however, S1 tumors were depleted of immune cells (immune deserts), while S...
Less than 10% of the total flows in all four waves were regarded as links in the dichotomized matrices. Network description Visualization with MDS We used “iterative metric multi-dimensional scaling (MDS)1” in NetDraw2 to generate coordinates based on similarity, adjusted to the nearest ...
After decomposing iEEG data into frequency bands of interest, we created correlation matrices across the spatial/spectral space of stimulation-evoked changes in power, and rank-ordered the output in terms of similarity for each stimulation configuration to the template patterns. Iterative model fitting...
This represents the similarity of expression patterns between a given pair of genes in the dataset, similar to the correlation matrix but taking into account their shared correlation with other genes. Finally, hierarchical clustering of the TOM is used to assign genes into modules based on their ...
The initiation of flowering is an important developmental transition as it marks the beginning of the reproductive phase in plants. The MADS-box transcription factors (TFs) FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) form a complex to repres
comparative assessment of the morphology of hemispermatophores across the whole order. Several phylogenetic analyses [45,46,47,48,49,50] subsequently used Stockwell’s work to define characters and character states of hemispermatophores for their respective matrices, but each of these studies focused...
“Secrebiome”. Notably, this represents 31.10% of the expression of the total metatranscriptome. From the 30,024 secreted proteins, 96.57% showed significant similarity against homologs in the NCBI’s non-redundant protein database (nr), 64.26% were assigned a Gene Ontology (GO) term, and ...
(Fig.1a). Indeed, there was no significant benefit to retaining more than 3 edges per gene (EPG3), while at this level of edge reduction the number of modules remained manageable for downstream analysis (Supplemental Fig.2a). Notably the use of parsimonious matrices in conjunction with Fast...
The initiation of flowering is an important developmental transition as it marks the beginning of the reproductive phase in plants. The MADS-box transcription factors (TFs) FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) form a complex to repres