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Integrating expression data across organisms is another promising approach to increase the accuracy of pathway discovery.
The task measured accuracy of pathway, economy of movement and time to task completion.
The accuracy of pathway inference can be further increased by iterating kWalks and/or by reducing the size of the sub-network extracted by kWalks in the first step of the hybrid.
To further assess the discriminatory accuracy of pathway biomarkers, we analyzed two large metastasis breast cancer data sets [ 3, 6], both obtained from primary breast cancer, but from non-overlapping populations.
To compare discriminatory accuracy of pathway biomarkers against individual gene biomarkers, for each training data set (i.e., a new training set with each sample that was left out) we selected the top 20 upregulated and top 20 downregulated pathways separating the metastatic and non-metastatic groups, using GSEA.
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We hope to involve the biomedical community as a means to improve the quality and accuracy of pathways in NetSlim and to keep them updated on an ongoing basis.
We compute the mean accuracy of a pathway by averaging the pathway classification results over all trials, using zero percent accuracy for any trial where a pathway was not represented.
As we did with the individual pathways, we compute the average validation accuracy of a pathway pair over the 50 trials, using zero percent accuracy for any trial where a pathway pair was not represented.
To address the accuracy of the pathway analysis we aimed to confirm the in silico generated hypotheses by experimental laboratory data.
After human curation, the accuracy of the pathway was proven through two tests.
However, the authenticity and accuracy of automatic pathway data curation and annotation is still under the scrutiny of various database developers and end-users.
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