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We found that the amount of regulatory control mediated by disease-associated microRNAs differs from pathway to pathway.
Because the nature and complexity of these interactions varied from pathway to pathway, a simple line connecting two pathways was used to represent their interaction.
The nature and complexity of these interactions varied from pathway to pathway, and for simplicity a line connecting two KEGG pathways was used to represent these interactions.
The studies performed thus far investigating how pathway structure restrains molecular evolution have shown that there exists a clear correlation between pathway topology and evolutionary rates of the system's proteins, however the specific relationship varies from pathway to pathway.
Even though the two pathways might share the identical genes, their function can vary from pathway to pathway, which would influence the number of corresponding small molecules that had been mined.
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LinkinPath infers the pathway-to-pathway connections using molecular interactions and reactions.
Its novel contributions such as functional composition using Treemaps, pathway-to-pathway interconnections and the global metabolic map with highlighting mechanisms add value over comparable existing tools.
The annotation results of input sequences can be interactively explored in different visualization perspectives including KEGG-pathway maps, TreeMaps, pathway-to-pathway networks and interaction and reaction paths.
On a solid blue edge in the pathway-to-pathway network, if the reaction paths exist, users can explore what enzymes and compounds are essential to a metabolic process via the reaction paths between two pathways (Supplementary Fig. S8).
Summary: LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networks and pathway-to-pathway networks.
Analyzing the effects of different mutational processes on pathway structure, we find that transitions from modular pathways to pathways with crosstalk are extensively caused by interaction addition (data not shown).
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