Fig. 5

Examples of the cis–trans regulatory correspondence between the polarized motif- and gene-eigenvectors. These examples are directly obtained from the human and dog CREF modules, and are supported by experimental evidence found in the literature. In each row, the right box displays certain major biological processes enriched at the poles of the fourth polarized gene-eigenvector; whereas the left box illustrates their transcription factors and binding cis-regulatory motifs near the poles of the fourth polarized motif-eigenvector of both humans and dogs. The two numbers in parentheses after the motif symbol indicate its rank in the fourth motif-eigenvector of humans and dogs, respectively. Motifs positioned at the negative pole are marked by negative ranks. The protein structures are from the AlphaFold Protein Structure Database^41,42. (A) Long-term memory and its four transcription factors with binding motifs. (B) Myelination and its four transcription factors with binding motifs. (C) Cochlea development and its four transcription factors with binding motifs.