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Fig. 2 | BMC Genomics

Fig. 2

From: Determining the optimal number of independent components for reproducible transcriptomic data analysis

Fig. 2

Analysis of reproducibility of previously identified metagenes in independent components of the METABRIC dataset. a,e,f,g,h show correlations (see Methods section) with the cell cycle, inflammation, myofibroblast, interferon signaling, immune-related metagenes from [3] as a function of the chosen data dimension M, and the stability of the best matched component. c shows the ratio between the correlation value of the proliferation metagene with the best matched component and the second best correlation (gap). d shows an intersection (Jaccard index) of the Freeman’s cell cycle signature [19] and the set of top-contributing genes (projection > 5.0) from the proliferation-associated independent component. b,i correlation of the cell cycle and immune-related metagene with the best matched component in the M = 100 ICA decomposition as a function of the stability-based component rank. In all plots, the vertical dashed line shows the MSTD value for the METABRIC dataset

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