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The highest ranked candidate month from Step 2 that meets the persistence criteria is used in the TMY.
Our analysis is validated by the fact that Acox1, a known COUP-TFI target [32], is among the highest ranked candidate target genes in our database.
For instance, the highest ranked candidate GPC1 (Wv-1.0, Ci-0.0) is shown to influence FGF2 signaling pathway [ 20].
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(3) Distractor candidate ranking The remaining candidates from the previous step are further ranked based on their closeness to the correct answer, and the three highest ranked candidates are utilised as the distractors.
The remaining candidates from the previous step are further ranked based on their closeness to the correct answer, and the three highest ranked candidates are utilised as the distractors.
Top 10 represents the probability that the correct MIDI file (corresponding to the input humming file) is included in the 10 highest ranked candidates among the 48 MIDI files [13, 17, 23].
In addition, to investigate whether the promoters of these selected gene probes are hypermethylated and this methylation is present in cancer and not in normal tissue, we determined the hypermethylation status of the 10 highest ranking candidate genes in both cervical cancers and normal cervices using COBRA (COmbined Bisulfite Restriction Analysis).
Besides using different techniques to evaluate the performance of ProSim, it was important to identify the relevance of high ranked candidate genes to a given query disease.
Prioritization of candidates like LPIN2 as high ranked candidates, clearly indicate the efficiency and importance of our method.
Biological Networks Gene Ontology tool (BiNGO), a plugin of Cytoscape software [ 11] was used to determine which GO terms are significantly overrepresented in a set of high ranked candidates.
The highest ranked novel candidate XLMR gene was TIMP1 (24/40 matches) that encodes a natural inhibitor of the matrix metalloproteinases (MMP), a group of peptidases involved in degradation of the extracellular matrix.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com