Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data

BMC Genomics

Table 3 Literature approval of the predicted TF complex formation from NFYA ChIP-seq data in HeLa S3 cells

Partner binding motif^a	Predicted partner^b	SpaMo p-value^c	Reference^d
E HeLa S3/FOS	FOS	5e-06	Fleming et al., [11]
E Sknsh/RFX5	RFX5	3.6e-05	Jabrane-Ferrat et al., [21]
E Hep G2/SREBP2	SREBP2	0.0015	Dooley et al., [22]
J NFIC	NFIC	0.0015	NA
J TBP	TBP	0.0076	Lee et al., [23]
E GM12878/TBLR1	SP1	0.014	Ravasi et al., [2]
E GM12878/CDP	SP1	0.015	Ravasi et al., [2]
E H1hesc/Rad21	Rad21	0.018	NA
J SP1	SP1	0.021	Ravasi et al., [2]
E K562/GTF2B	TBP	0.022	Lee et al., [23]
E Hep G2/MAZ	SP1	0.023	Ravasi et al., [2]

^aThe source of the partner binding motif. Summary names are used in the first column, in which “E HeLa S3/FOS” indicates the secondary motif from the ENCODE FOS ChIP-seq sample in the HeLa S3 cell line, and “J NFIC” indicates the motif from the JASPAR NFIC motif
^bThe list of the NFYA-partner TF complexes
^cThe p-value for the significant spacing of the binding motifs from SpaMo
^dThe external studies that support the existence of the TF complex
NA: reference is not available

ISSN: 1471-2164