This track shows statistically significant matches between the human genome and motifs from the TRANSFAC 10.2 motif database. The quality of each match is summarized as a q-value, defined as the minimal false discovery rate threshold at which the match would be deemed significant. Only matches with a q-value ≤ 0.1 are shown.
The score is the q-value for the motif, mapped into the range 0-1000 using the function
score = min(400 - 100 * log10(q), 1000)
This track was generated using tools from the MEME Suite. First, fasta-get-markov was used to generate a 0th order Markov model for the background frequencies of the nucleotides in the human genome (omitting the Y chromosome and the mitochondrial genome). The resulting model assigns the following background probabilities: A/T=0.2955, C/G=0.2045 Second, the TRANSFAC 10.2 motif database was converted into MEME format. using the transfac2meme transfac2meme utility. Third, FIMO version 4.6.1 was used to scan the human genome with each of the TRANSFAC motifs, using the background model and a p-value threshold of 1e-6. The FIMO results for all the motifs were concatenated, matches with q-value > 0.1 were eliminated, and the results converted to BED format.
No verification was performed.
This is the initial release of this track.
Charles E. Grant, Michael M. Hoffman, Timothy L. Bailey, William Stafford Noble
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble
FIMO: scanning for occurrences of a given motif
Bioinformatics (2011) 27(7): 1017-1018 first published online February 16, 2011 doi:10.1093/bioinformatics/btr064
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D,
Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E.
(2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.
Nuc Ac Res 34(Database issue):D108-110