Documentation
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Methods:
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Prediction of transcription factor binding sites with Motevo algorithm:
Finding regulatory elements and regulatory motifs: a general probabilistic framework.
Erik van Nimwegen
BMC Bioinformatics 2007 Sep 27; 8 Suppl 6:S4
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Annotating of promoteroms (transcription start sites, transcription start clusters and transcription start regions):
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data
Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen EJ
Genome Biol. 2009 Jul 22;10(7):R79
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Construction of position specific weight matrices
from supplementary materials of:
The
transcriptional network that controls growth arrest and differentiation in
a human myeloid leukemia cell line
FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO,
Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, et al
Nat Genet. 2009 May;41(5):553-62
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Formats:
