TY - GEN
T1 - A novel application of mixing coefficients for reverse-engineering gene interaction networks
AU - Singh, Nitin
AU - Ahsen, M. Eren
AU - Mankala, Shiva
AU - Vidyasagar, M.
AU - White, Michael A.
PY - 2012
Y1 - 2012
N2 - In this paper, we present a new application of the so-called phi-mixing coefficient between two random variables. Using the phi-mixing coefficient, as well as an analog of the well-known data processing inequality from information theory, we present a new algorithm for reverse-engineering gene interaction networks (GINs) from expression data, by viewing the expression levels of various genes as coupled random variables. Unlike existing methods, the GINs constructed using the algorithm presented here have edges that are both directed and weighted. Thus it is possible to infer both the direction as well as the strength of the interaction between genes. Several GINs have been constructed for various data sets in lung and ovarian cancer. One of the lung cancer networks is validated by comparing its predictions against the output of ChIP-seq data.
AB - In this paper, we present a new application of the so-called phi-mixing coefficient between two random variables. Using the phi-mixing coefficient, as well as an analog of the well-known data processing inequality from information theory, we present a new algorithm for reverse-engineering gene interaction networks (GINs) from expression data, by viewing the expression levels of various genes as coupled random variables. Unlike existing methods, the GINs constructed using the algorithm presented here have edges that are both directed and weighted. Thus it is possible to infer both the direction as well as the strength of the interaction between genes. Several GINs have been constructed for various data sets in lung and ovarian cancer. One of the lung cancer networks is validated by comparing its predictions against the output of ChIP-seq data.
UR - http://www.scopus.com/inward/record.url?scp=84875733385&partnerID=8YFLogxK
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U2 - 10.1109/Allerton.2012.6483391
DO - 10.1109/Allerton.2012.6483391
M3 - Conference contribution
AN - SCOPUS:84875733385
SN - 9781467345385
T3 - 2012 50th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2012
SP - 1461
EP - 1466
BT - 2012 50th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2012
T2 - 2012 50th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2012
Y2 - 1 October 2012 through 5 October 2012
ER -