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For Alzheimer's disease, we analyzed the outcome of the frequency based ranking method and calculated the precision, F-score and rank for different recall ranges (10%, 30%, and 50% recall) and determined the maximal F-score (see Table 3).
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Microcalorimetric Tm based ranking was then compared with the long term stability ranking.
Table 2 shows that top 10 ranked interactions from the frequency based ABC model using CTD entities information.
The 9th ranked and 10th ranked ones were different between the hybrid and the frequency based approach.
The first one is frequency based in which each gene is awarded a rank in accordance with the occurence of mutation which means the higher the frequency of occurence of mutations on that gene, the higher rank will be awarded.
For the comparison, we analyzed the top 10 ranked results of the cosine similarity based hybrid method and the frequency based ABC method.
The literature based analysis of top 10 ranked interactions confirms that our hybrid based approach could find more meaningful interactions than the frequency based ABC model.
We reported allele frequencies based on the frequency of the majority allele.
Overall, frequency-based ranking seems to perform better than relative entropy-based ranking.
When comparing the frequency-based ranking to the set of genes in the published 70-gene and 231-gene signatures, there appear to be additional genes with high frequencies of occurrence that were not part of the published signatures.
Concerning the statistical ranking of the result set, the frequency-based ranking method performs better than the relative entropy-based ranking for biomarker gene enrichment of the diseases investigated in this study.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com