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.

StandfuƟ et al.

StandfuƟ et al. BMC Cancer 2012 12:380   doi:10.1186/1471-2407-12-380

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