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To avoid a connectivity bias related to the possible presence of target vertices with high degrees in contrast with random vertices we restricted the list of genes from which we randomly take a vertex.
Raemaekers and colleagues discuss the lack of a radial/tangential distinction in their discussion: "The results regarding a radial/tangential connectivity bias were inconclusive" (see Raemaekers et al., 2014, p. 919).
Although this interpretation fits very well with physiological data suggesting a connectivity bias favoring interneurons versus pyramidal cells, it needs to be taken into account that excitatory synapses onto pyramidal cell dendritic shafts are extremely rare in SO and SR, but may occur, albeit in limited numbers, in the SLM (Megías et al. 2001).
Some of the coarse-scale networks that were detected with ICA contained features that would either contribute to a radial or tangential connectivity bias, and this may have obscured results in the initial analysis… The fluctuations within these (radial/tangential) networks were, however, filtered from the data in the second analysis, which may have attenuated the observed effect".
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This method is also subject to connectivity biases of each gene product causing highly connected genes to be counted in more paths.
The enrichments of GWAS genes, cancer genes, mouse knockout phenotypes, therapeutic targets, and biomarkers was also controlled for connectivity biases.
Interestingly, ancestral nodes associated with mammalian and chordate duplications exhibited even higher connectivity biases, but the progeny of these genes were not associated with human hubs.
This method uses a graph permutation algorithm to create a null distribution that takes into account connectivity biases of the known interactome to identify genet sets with statistically enriched interactions between RNAi targeted gene products.
Moreover, the effect of duplicate genes on mouse genetic robustness is duplication-age dependent, which holds after ruling out the potential confounding effect from coding-sequence conservation, protein-protein connectivity, functional bias, or the bias of duplicates generated by whole genome duplication (WGD).
Previous studies on Boolean networks mostly assume several parameters as important from the very beginning (such as connectivity or bias) and use those to identify dynamics or robustness properties.
When there is more than one function represented by classified proteins in the cluster, use a combination of connectivity and preference bias information (7-NEIGHCONNECT) for prediction.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com