kebabsData: KeBABS Sequence Data
Description
The package contains two small sequence datasets for demonstration of the
package functionality.
TFBS is a subset of EP300/CREBBP binding data provided with the publication
Lee et al., 2011. The data is based on binding sites identified with
ChIP-seq by Visel et al., 2009. Please note that due to package
size restrictions only a small subset of the data used in Lee et al., 2011
is included in the package. Following variables are defined:
enhancerFBcontains 259 DNA sequences of tissue specific
enhancers from embryonic day 11.5 mouse embryos and 241 negative sequences
sampled from mm9 genome.yFBcontains the associated labels
CCoil is a set of heptad-annotated amino acid sequences of coiled coil
proteins forming dimers or trimers from the web site of the package
PrOCoil by Mahrenholz et. al., 2011. The data contains the sequences
with heptad annotation, the oligomerization state and group assignment for
each sequence. The grouping was performed through single linkage clustering
of sequence similarities based on pairwise ungapped alignment. Following
variables are defined:
ccseqcontains 477 AA sequences of heptad-annotated amino acid
sequences with a minimum length of 8 and a maximun length of 123 AAs.yCCcontains the associated oligomerization state "DIMER" or
"TRIMER".ccannotis a charcter vector with the heptad annotations for
the sequences. Characters 'a' to 'f' represent specific positions within the
coiled coil structure. The AA string set already contains the annotation
as metadata. But for demonstration purpose it is available as separate data
item.ccgroupsis a numeric vector containing the group numbers of
of the sequences.
format
TFBS contains the 259 positive and 241 negative sequences as
DNAStringSet and the corresponding labels as numeric vector containing a
value of 1 for positive and -1 for negative samples.CCoil contains the 477 AA sequences as AAStringSet and the corresponding
labels as factor. The heptad anntoation is stored as character vector and
group assignment as numeric vector.
source
TFBS: http://www.beerlab.org/p300enhancer
CCoil: http://www.bioinf.jku.at/software/procoil/data.htmlReferences
(Lee, 2011) -- D. Lee, R. Karchin and M. A. Beer. Discriminative prediction
of mammalian enhancers from DNA sequence. Genome Research, 21(12):2167-2180,
2011.
(Visel, 2009) -- A. Visel, M. J. Blow, Z. Li, T. Zhang, J. A. Akiyama,
A. Holt, I. Plajzer-Frick, M. Shoukry, C. Wright, F.Chen, V. Afzal,
B. Ren, E. M. Rubin and L. A. Pennacchio. ChIP-seq accurately predicts
tissue-specific activity of enhancers. Nature, 457(7231):854-858, 2009.
(Mahrenholz, 2011) -- C. Mahrenholz, I. Abfalter, U. Bodenhofer, R. Volkmer
and S. Hochreiter. Complex networks govern coiled-coil oligomerizations -
predicting and profiling by means of a machine learning approach.