Assessing Clusters and Motifs from Gene Expression Data

Table 2.

Forkhead Transcription Factor DNA-Binding Motifs

Protein Organism Consensus sequence
Freac-2 Human N N A N N G T A A A C A A N N N
Freac-3 Human N N N N N G T A A A T A A A C A
Freac-4 Human C Y W A W G T A A A C A N W G N
Freac-6 Human T A A A Y A A A Y A N N M
Freac-7 Human W N N A N A T A A A Y A N N N N
HFH-8 Mouse Y R N A T A A A C A N N N
HFH-1 Rat A W A T A A A C A W T N
HFH-2 Rat A A A Y A A A C A W T N
HNF-3β Rat W A A R Y A A A Y A N T N C M
XFD-1 Xenopus laevis Y A W G T A A A Y A W W R Y
XFD-2 X. lae. W N W A T A A A C A W N N R
XFD-3 X. lae. W N W G T M A A C A W W M W
Croc Drosophila melanogaster W A N A R T A A A T A T N N N N
HCM1p Yeast W A A Y A A A C A A W
ECB-SFF Yeast A A W W N R T A A A Y A A A
SFF-LIKE Yeast W A W W N R T A A A C A A N
M14b Yeast W N W A A A H A A A C A M W
  • Note. Weight matrix consensus sequences (IUPAC codes) taken from Transfac (Wingender et al. 2000) unless noted otherwise. References for the motifs taken from Transfac are given in the text.

  • Zhu and Davis (1998).

  • Spellman et al. (1998).

  • This work.

  • Tavazoie et al. (1999).

This Article

  1. Genome Res. 11: 112-123

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