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Fig. 2 | Genome Biology

Fig. 2

From: Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Fig. 2

Differential co-expression analysis of an example network with 150 genes and 500 samples. a The regulatory network used to simulate the data and the two knockdown genes (KDs) (orange and purple nodes). b A differential co-expression (DC) network inferred from the simulated data using the z-score method. Interactions shown have significantly different correlations between knockdown and wildtype states (FDR < 0.1). Correct predictions for each knockdown as per the “true” differential association network are coloured respectively with false positives in grey. c Three representations of the true co-expression network obtained from a perturbation analysis of the regulatory network. Direct differential interactions are a subset of differential influences which are in turn a subset of differential associations. d Empirical z-transformed correlations for each interaction in the respective “true” networks. The association network shows a similar correlation profile to the direct and influence networks but with added points, as shown for example by the circled points

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