Fig. 1
From: Saltations of cis-regulatory modules in Canidae and Hominidae
The scheme of the CREF dual eigen-analysis. (1) The species-specific cis-regulatory elements frequency (CREF) matrices of five canids: dog, dingo, red fox, dhole, and wolf. The CREF matrix is a systematic representation of the cis–trans binding strengths in the proximal regulatory region of all protein-coding genes. (2) The singular value decomposition (SVD) of the CREF matrix. The CREF matrix is stratified into multiple levels. Each level has a singular value, a gene-eigenvector, and a motif-eigenvector. (3) Polarization of eigenvectors by sorting their loadings. Each pair of polarized gene- and motif-eigenvectors, together with the singular value comprise a CREF dual eigen-module. (4) Inferring the regulator-target of each CREF dual eigen-module by enrichment analysis on the polarized gene-eigenvectors and motif analysis on the polarized motif-eigenvectors. (5) Identification of the saltation by the integration of CREF modules. The integration mainly consists of the evaluation of module conservation and analysis of module stability.
