A GUIDED SAMPLING ALGORITHM FOR IDENTIFYING NETWORK
MOTIFS IN A TRANSCRIPTION REGULATORY NETWORK
cs Center, Institute for Chemical Research,
Kyoto University, Gokasho, Uji,
The identification of network motifs is an important problem in bioinformatics due to its
complexity and application to other areas. N
etwork motifs are statistically
subgraphs when compared to
a random network
[Milo et al., 2002]
Milo et al.
that the technique used for transcription regulatory networks can also be applied to
artificial networks such as electronic circuits and links between Web documents. One
refinement to their brute
orce technique involved random sampling
[Kashtan et al.,
In this poster, we describe some work
progress which is an extension to the random
sampling approach. Determining whether or not a network motif is statistically
significant depends on the
number of samples taken. However, the fact that graphs such
as transcription regulatory networks contain local clusters
Randrup et al., 2004]
has motivated us to investigate the possibility of guiding the sampling process.
Essentially, not all v
ertices in the graph are equal. We apply a scoring mechanism to
each vertex based on the number of directed edges it and its neighbors contain. Then
group the vertices into
buckets based on the distribution of the scores. By sa
ortion from each bucket, there is an approximately equal probability of
sampling vertices from regions of high and low connectivity. Preliminary experiments
with the transcription regulatory network of
shown that the feed
ied by others
[Milo et al., 2002]
located by our method usin
% of the vertices. In the future, we plan to expand our experiments to other
data sets and explore other vertex scoring mechanisms in order to refine our technique.
J. Fleishman, N.
Tal, and L.
Comment on `
Building Blocks of C
etworks' and `
Evolved and Designed N
N. Kashtan, S. Itzkovitz, R. Mi
lo, and U. Alon. Efficient
R. Milo, S. Shen
Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon. Network
These authors contributed equally to this work.