Our focus is on network analysis and modeling, integrated with cancer profiles that will enable us to identify diagnostic and prognostic biomarkers, understand disease initiation and progression, which will lead to improving cancer treatment. Our tools, such as NAViGaTOR, I2D and BTSVQ enable users to interpret integrated cancer profiles, and create relevant models dynamically.
NAViGaTOR
is a
software package for visualizing and analyzing protein-protein
interaction networks. NAViGaTOR can query OPHID / I2D - online
databases of interaction data - and display networks in 2D or 3D. To
improve scalability and performance, NAViGaTOR combines Java with
OpenGL to provide a 2D/3D visualization system on multiple hardware
platforms. NAViGaTOR also provides analytical capabilities and supports
standard import and export formats such as GO and the Proteomics
Standards Initiative (PSI).
In protein-protein interaction networks, nodes represent proteins, and edges between nodes represent physical interactions between the proteins.These visualizations can enable insights into the proteins that play key roles in diseases such as cancer.
Go to NAViGaTOR home page
I2D
is an on-line database of known and predicted mammalian and eukaryotic
protein-protein interactions. It has been built by mapping
high-throughput (HTP) data between species. Thus, until experimentally
verified, these interactions should be considered "predictions".
I2D remains one of the most comprehensive sources of known and
predicted eukaryotic PPI.
Go to I2D home page
BTSVQ
is a computational tool to analyze and visualize microarray gene
expression data. This technique merges the results of SOM (genes
space), and partitive k-means (specimen space). The algorithm uses
vector quantization and self-organizing capabilities of SOMs in finding
significant gene centers in gene space (high dimensionality and large
number of clusters), and the effectiveness of k-means in experiment
space (medium dimensionality and low number of clusters).
Go to BTSVQ home page