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Using a novel relaxation method to further refine this set, they ended up with a library of decoys consisting of 650 structures on an average for each protein.
We sought to refine this set further and identified subsets of approximately 50 genes (including copy number and expression features) that best defined each of the five iCluster groups (see Suppl. methods).
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To eliminate any shared polymorphism due to repeated mutations, we refined this set further by considering only shared haplotypes with at least two shared SNPs.
As a representative, the widely used k-means clustering begins with an initial set of randomly selected centers and then iteratively refines this set to decrease the sum of the squares distances.
Besides these theoretical contributions, on the practical side, refining this set of forty-two constructs down to just twenty-two makes way for training procedures that are better suited to the reality of small companies.
In Section 2.2, we will describe an algorithm that further refines this set of matches, to determine the placement of sequences that do not have a unique mapping.
Existing studies in breast cancer have involved three steps: identifying a set of genes that are different between survival or drug response, refining this set for optimal classification within the sample set and finally validating the performance of the classifier genes on independent samples.
The third input parameter for ISA is the number of starting points that the algorithm uses for randomly selecting a set of genes and iteratively refining this set until the genes and conditions in it are mutually consistent and match the definition of a transcription module.
To refine this data set, we carried out a genome-wide RNAi viability screen in the same cell line providing z-scores for viability of 16,363 genes.
To further refine this gene set, we then interrogated the Oncomine compendium of expression array data to determine which of these 97 genes are significantly overexpressed in at least three additional independent prostate cancer datasets when a Top 1% overexpression threshold was applied together with a p-value threshold of 1x10−4 [ 25].
We used T. spiralis and R. culicivorax gene sets to refine and restrict this set of phylotypic stage genes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com