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Finally, we included in our study large datasets contained in the ENCODE database.
SNiPA includes a wide range of genome-level datasets contained in the Ensembl database (Flicek et al., 2014) as an established backbone of annotations for the human genome.
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We have used the dataset contained in AnEnΠ (Analogous Enzyme Pipeline), which was obtained from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database (from ftp://ftp.genome.ad.jp/pub/kegg/ of December, 2006) [ 39].
The existence of large datasets such as that contained in the NCBI Gene Expression Omnibus (GEO) repository [ 5] provides an opportunity to identify such probes.
Testing the performance (predictive accuracy and run time) of the proposed methods, requires evaluating them over datasets with different properties such as (1) number of samples contained in the dataset, (2) number of cancer types contained in the dataset, and (3) the similarity level between samples from different cancer types, which indicating the difficulty of classification.
In addition to the variables contained in the datasets, we will gather additional information about the datasets to allow us to evaluate particular sources of heterogeneity through meta-analyses of refined subsets of the datasets.
We used two datasets contained as examples in the PROAST software (RIVM 2012) to illustrate the approach: BW changes in rats and forestomach tumors in male mice.
However ML is sensitive to the samples contained in the dataset; changes in the dataset may alter the manifold structure.
Arithmetic mean and median MCC of a whole dataset are calculated from the mean MCCs of all interactions contained in the dataset.
In the table, the number of hits for each dataset matching the GO categories contained in the GO slim, normalized to a sample dataset of 30,000 sequences, is displayed.
A two-step process reveals the information contained in the datasets.
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