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b) Using a length filter, we show only the pathways that are greater than 40mm in length (30percentt of the total number of pathways).
The total number of pathways identified as non-randomly targeted is striking.
At the end of this procedure, each sample will be associated with n L-values, and each pathway will assigned to m L-values, with n and m representing the total number of pathways and number of samples respectively.
Let N be the total number of pathways in human.
Percentages are relative to the total number of pathways and total number of enriched pathways respectively.
For the total number of pathways, only two tests gave better results than the 183 genes of interest selected by the methodology.
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The total number of pathway holes was 593, or 56% of the total known reactions in pathways.
Ratio shows the relative overlap between number of molecules per pathway within each dataset over the total number of pathway-specific molecules present in Ingenuity Knowledge Base.
The total number of pathway holes as a percentage of total reactions in pathways is 14%, which is higher than EcoCyc (5%), but lower than the existing version of HumanCyc (36%).
For each blood stage and each metabolic pathway the fraction of consensus reactions per total number of pathway reactions was computed to uncover the distribution of consensus reactions among pathways (see Additional file 17).
The recall is computed as a/k, where k is the total number of pathway genes that were scored by the MSGR. The average of the precision and recall is taken across the cross-validation folds to obtain an average precision and an average recall for a single pathway.
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