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Gene clustering and GO enrichment analysis within clusters was performed in STEM [ 40] using default parameters (STEM Clustering Method).
The differential gene expression between the significant clusters was performed using the Welch's t-test implemented in the multtest package.
A complete analysis of these clusters was performed, enabling prediction of likely products in most cases (Materials and Methods and File S1).
The elimination of the singleton clusters was performed only for the aforementioned evaluation of the degree of redundancy in the dataset.
Detection of BTFC and YLF gene clusters was performed using a multiplex real-time PCR melt procedure as previously described [6].
Identification of overrepresented functional categories among 1663 high-fat responsive genes and their grouping into functionally related clusters was performed using DAVID Functional Annotation Clustering tool [29].
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Time division between clusters is performed as follows.
Clustering was performed through k-means cascade algorithm.
Supervised clustering was performed.
Hierarchical clustering was performed using dChip software.
B-RLMM clustering was performed with 94 samples per cluster.
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