SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer

Table 3 Motif annotations

Motif	GO term predictions	Motif match
1	BP - positive regulation of transcription	no match
	from RNA polymerase II promoter
	BP - transcription
	BP - negative regulation of transcription
	from RNA polymerase II promoter complex
	MF - transcription activator activity
2	MF - transcription factor activity	Zfp740, Zfp281,
	MF - sequence-specific DNA binding	Sox13, Sp4,
	BP - transcription	Pitx3, Smad3,
	BP - inner ear morphogenesis	Egr1, Ascl2,
	BP - proximal/distal pattern formation	Zfp410
3	no prediction	Spdef, Tcfe2a
4	no prediction	Zbtb3
5	MF - sequence-specific DNA binding	no match
	MF - transcription factor activity
	BP - positive regulation of transcription from
	RNA polymerase II promoter
	MF - calcium ion binding
6	MF - receptor binding	Gm397
	BP - axon guidance
	BP - positive regulation of immune response
	BP - defense response

Motifs found by motif search in 285 segments of the Tumor1 sample are depicted in Figure 6. GO term associations using GOMO [40] and the motif matches against the UniProbe [42] database using TomTom [41] were computed for each motif. In cases of motif 1, motif 2, motif 5 and motif 6 Gene Ontology term associations were found. Biological processes are abbreviated by BP, molecular functions by MF. Nine motifs of the UniProbe database match motif 2 and only two UniProbe motifs match motif 3.

ISSN: 1471-2407