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Interestingly, while the modules are expected to represent highly related functions, it has been observed [ 33] that known pathways in metabolic networks do not correspond to top-scoring modules, as large pathways are composed of smaller units which are mixtures of sub-structures associated to different pathways.
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However, when diagrams become large, pathways be rotated and viewed from any angle, zoomed in on and generally manipulated in an environment which is quite different to that of any 2D representation.
An integrated pathway map that connects all subdivided pathways into a single large pathway is more suitable and intuitive as a context for information mapping rather than rotating through hundreds of specific maps.
Suppose that only a small portion of a large pathway is involved, standard statistical tests would fail.
One database (BioCyc) may emphasize on some very specific aspects of a certain large pathway; so this large pathway is broken up in this database into different pathways with similar/related names, yet all describing the detailed aspects of the original large pathway; see Table 6.
We notice that the largest pathway is H+ formation, which is in agreement with the experimental yield as the H+ ion peak is the strongest.
Selecting the hub's name, as opposed to that of the largest pathway, was chosen since this tends to enhance the descriptive value for the entire SuperPath.
For the PCA this reduction is much more dramatic – 53% and 40% respectively, suggesting that the mapping function between cues and responses becomes more non-linear when large signaling pathways are considered.
The Isomap projection performs slightly worse when more signaling networks are analyzed; suggesting that the mapping function between cues and responses becomes increasingly non-linear when large signaling pathways are considered.
Properties of the small- and large-pore pathways are exhaustively reviewed elsewhere [ 22, 140, 171].
Second, a large number of pathways are shared by both phases.
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