Fig. 3: Evaluation of the performance of TRAPT in TR knockdown/knockout experiments on differential gene sets from the KnockTF database. | Nature Communications

Fig. 3: Evaluation of the performance of TRAPT in TR knockdown/knockout experiments on differential gene sets from the KnockTF database.

From: TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data

Fig. 3

a The bar chart represents MRR scores of the model after each module was removed. Higher scores reflect better performance. b The grouped bar chart shows the first, five, and 10 highest-ranking TRs that were correctly predicted. We progressively removed U-REA, D-RP, and the specific TR-RP model to assess the impact of each module on model performance. c The bar chart represents MRR scores of TRAPT, where “TRAPT-KD” refers to the use of knowledge distillation and “NKD” refers to the model without knowledge distillation. d The number of target TRs accurately identified among the top 10 using the specific and basic regulatory potential models. e Evaluation of the performance of the KD-TRAPT model and the NKD-TRAPT model using Lisa benchmark data. f Sunburst chart displaying the MRR scores of all TRs in the upregulated and downregulated gene sets. The top-ranking TR is highlighted. g The scatter plot, where the size of the points represents the normalized MRR scores of target TRs. The right side displays the normalized MRR scores for the upregulated and downregulated groups in the TRAPT-H3K27ac epigenetic model and the TRAPT-ATAC epigenetic mode. The left side of the plot shows the normalized MRR scores of TRAPT along with the peaks in the promoter model for the upregulated and downregulated groups. Red and blue dashed lines correspond to the upregulated and downregulated sets, respectively. The gray dashed line indicates the baseline reference, while points overlapping with the lines represent consistent performance between the two methods. h Bar chart representing MRR scores of the model after the removal of each epigenetic feature. The last bar represents the peak-in-promoter model once all epigenetic modules of TRAPT had been removed. i Scatter plot illustrating the predicted ranking of the TRs. The left side represents upregulated gene sets while the right side represents downregulated gene sets. CTCF, NANOG, FOXA1, and ESR1 had high ranks in both the upregulated and downregulated gene sets, indicating their potential dual functions as transcriptional activators and repressors.

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