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Fig. 2 | BMC Systems Biology

Fig. 2

From: Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators

Fig. 2

Standard gene expression analyses are not sufficient to identify drivers. a Heatmap depicting 25 gene expression clusters in 30 strains of rapamycin-sensitive yeast over six time points. Red and blue colors represent, respectively, positive and negative standardized expression (mean-subtracted and normalized by standard deviation in a row-wise manner) that has been averaged over the genes in each cluster. Examples of enriched GO terms are provided for selected clusters. Rows are labeled by cluster numbers as defined in Additional file 2. b Venn diagram shows the overlap between the top 10 % differentially expressed genes (DEGs) and the driver genes present on the array. P-value is from Fisher’s exact test. Number in blue denotes number of genes in universe not counted inside the Venn diagram. Top plot depicts the significance of the overlap as the number of DEGs is varied. Red dashed line indicates the minimum value for statistical significance. Bottom plot shows the receiver-operator characteristic (ROC) for the ranked list of DEGs and its overlap with driver genes. Dashed black line indicates expected ROC from random chance. P-value corresponds to a Kolmogorov-Smirnov test. c Venn diagrams indicating overlaps between driver transcription factors (TFs) and either the enriched TFs in all clusters, or from DREM analysis. P-values are from Fisher’s exact test. Number in blue denotes number of genes in universe not counted inside the Venn diagram. Plot shows the output of DREM with the master regulators listed on top of expression profiles of target gene clusters

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