What
is EXCAVATOR
EXCAVATOR is a computer software for gene
expression data clustering. It employs a set of unique clustering
algorithms developed by the Protein Informatics Group of
Oak Ridge National Laboratory. Unlike any existing gene
expression analysis tools, EXCAVATOR represents a set of
gene expression data as a minimum spanning tree (MST), a
concept from the graph theory. We have rigorously proved
that the MST representation, though simple in its structure,
did not lose any essential information for the purpose of
the data clustering. Through this representation, we have
reduced a multiple-dimensional data clustering problem to
a tree partitioning problem, a much simpler problem computationally.
The MST representation facilitates
-
efficient implementations of clustering
algorithms with guaranteed mathematical properties,
including global optimality;
-
including global optimality;
-
strong capabilities in handling data
clusters with complex cluster boundaries; and
-
strong capabilities in overcoming problems
caused by background noise.
Features
-
clustering gene expression profiles
under various definitions of distances and clustering
algorithms;
-
data-constrained clustering;
-
automatic selection of the most plausible
number of clusters in a data set;
-
removal of background noise;
-
identification of gene with similar
expression profiles to a set of specified seed genes;
and
-
comparison of clustering results using
different clustering parameters and algorithms.
Reference
If you use EXCAVATOR, please refer to:
Ying Xu, Victor Olman, and Dong Xu. Clustering
Gene Expression Data Using a
Graph-Theoretic Approach: An Application of Minimum Spanning
Trees. Bioinformatics.
In press.
Bug Reports
Please
email us any bugs of the program.
Copyright / Availability
The program EXCAVATOR is copyrighted and
is NOT in the public domain. Please contact
us
about the download information. EXCAVATOR is free of charge
to academic users. For
commercial users, please send
us an email for more information.
The authors of EXCAVATOR make no representations
about the suitability of the software
for any purpose. It is provided "as is" without express or
implied warranty. The authors shall not
be liable for any damages suffered by Licensee from the use
of this software.
Acknowledgment
The development of EXCAVATOR was sponsored
by the Office of Biological and Environmental Research, U.S.
Department of Energy, under Contract DE-AC05-00OR22725, managed
by UT-Battelle, LLC.
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