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It comprises three stages: (i) dataset collection and pre-processing, (ii) candidate genes extraction and (iii) manual verification.
The same progressive displacement from unstable CD34+HPCs attractor is highlighted with the Changed Sequences and with a random 250 genes extraction.
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We adopted four different choices of genes extractions as basis for computing autocorrelation with t0 state vector: entire genome, only cytokine, random extraction of genes, and 'connector' genes respectively.
Filtering of genes based on r-square (>0.8) was performed and 'vars' was set at 'each', generating as many significant genes extractions as variables in the general regression model.
The two-colour spotted array data of Haqq et al. was used as provided by the authors in Supplementary Table 10 of their paper [14], and converted to a GenePattern GCT-formatted file for gene extraction and hierarchical clustering (Pearson correlation, average linkage, median-centred).
BY performed culture, treatment and gene extraction.
Our system has multiple components including text preprocessing, gene extraction, feature construction and distant supervision.
For gene extraction, a multiple-testing corrected t-test (the so-called q-value) is employed.
The evaluation of target-gene extraction during each step was carried out using an index termed "Enrichment" (see Methods section).
Since microarray expression data include lots of false positives, methods that allow for further gene extraction from the set of differentially expressed genes are required.
After stringent washing, the fluorescent signals were scanned with a 3D-Gene Scanner (Toray Industries Inc). and analyzed using 3D-Gene Extraction software (Toray Industries Inc).
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