Table 1 Summary of the main cis-regulatory grammar findings for each TFBS in homotypic and heterotypic clusters

From: Transcription factor binding site orientation and order are major drivers of gene regulatory activity

Homotypic

Copy Number

Upregulate: AP1, CEBPA, FOXA1, HNF1A, HNF4A, PPARA, SP1, XBP1; Downregulate: CREB1, CTCF, GABPA, REST, TFAP2C, ΥΥ1

Orientation

AHR, FOXA1, HNF4A, NR2F2, ONECUT1, PPARA, REST, RXRA, SP1, TFAP2C, XBP1, YY1

Orientation +Copy Number

Consistent expression levels across copy number and orientations:HNF1A, AP1, CTCF, GABPA, YY1, REST; Consistent expression levels across copy number and one orientations: AHR, CEBPA, TFAP2C, HNF4A, PPARA; Antithetical expression levels across copy number and orientations: ONECUT1, RXRA, FOXA1, XBP1

Distance from TSS

Upregulate: AHR, CREB1, CTCF, GABPA, HNF1A, REST, SP1, XBP1, YY1; Downregulate: FOXA1 and ONECUT1

Distance from TSS + Orientation

Consistent expression levels across distance and orientations: CEBPA, AHR, HNF4A, PPARA, REST, XBP1; Consistent expression levels across distance and one orientations: CTCF, HNF1A, AP1,GABPA,TFAP2C,SP1,ONECUT1,RXRA,FOXA1; Antithetical expression levels across distance and orientations: None

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