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Fig. 6 | BMC Bioinformatics

Fig. 6

From: Visualizing complex feature interactions and feature sharing in genomic deep neural networks

Fig. 6

Visualization of sequence features captured by the 480 channels in 2nd convolutional layer of DeepSEA. The sequences are generated using gradient ascent (see section 1). The matrix represents -log10 of TOMTOM Q-values for each pair of channel and its top matching motifs. Each row represents a known JASPAR motif which has been ranked as top 1 matching motif for at least one of the channels. Only pairs that achieve less than 0.005 Q-value are represented with actual Q-value, and the dark blue region represents default value for low Q-values. In the right panel, the left column shows the SeqLogo visualizations of representative gradient ascent outputs of 5 of the channels, and the top matching motifs are shown in the right column. Channel 116 and 451 captures single motif of Alx4 and MafG. Channel 280 captures 3 consecutive motifs (GATA1,Myod1 and GATA2), while channel 77 captures consecutive NFYB/YA motif and its reverse compliment. Channel 179 captures either REST or its reverse compliment depending on the input sequences used for initialization

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