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COpy Number and EXpression In Cancer (CONEXIC) is an algorithm that
integrates matched copy number (amplifications and deletions) and gene
expression data from tumor samples to identify driving mutations and
the processes they influence. CONEXIC is inspired by Module Networks
(Segal et al, 2003), but has been augmented by a number of critical
modifications that make it suitable for identifying drivers. CONEXIC
uses a score-guided search to identify the combination of modulators
that best explains the behavior of a gene expression module across
tumor samples and searches for those with the highest score within
the amplified or deleted region.
When using CONEXIC, please cite the following article:
Akavia, U.D.*, Litvin O.*, Kim J., Sanchez-Garcia F., Kotliar D., Causton H.C., Pochanard P., Mozes E, Garraway L.A., Pe'er D. An Integrated Approach to Uncover Drivers of Cancer. Cell 2010; 143:1005-1017
*Equal Contribution
You can read detailed usage instructions here. A tutorial is available.
In order to run CONEXIC, please download
it as well as the math commons library
(see http://commons.apache.org/math/
for more detail about this library).
For any questions, please contact conexic@gmail.com.
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