Inference of large-scale gene regulatory networks using regression-based network approach.
The gene regulatory network modeling plays a key role in search for relationships among genes. Many modeling approaches have been introduced to find the causal relationship between genes using time series microarray data. However, they have been suffering from high dimensionality, overfitting, and heavy computation time. Further, the selection of a best model among several possible competing models is not guaranteed that it is the best one. In this study, we propose a simple procedure for constructing large scale gene regulatory networks using a regression-based network approach. We determine the optimal out-degree of network structure by using the sum of squared coefficients which are obtained from all appropriate regression models. Through the simulated data, accuracy of estimation and robustness against noise are computed in order to compare with the vector autoregressive regression model. Our method shows high accuracy and robustness for inferring large-scale gene networks. Also it is applied to Caulobacter crescentus cell cycle data consisting of 1472 genes. It shows that many genes are regulated by two transcription factors, ctrA and gcrA, that are known for global regulators.
Kim
Haseong
H
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, San 56-1, Shilim-dong, Korea. khs123@snu.ac.kr
Lee
Jae K
JK
Park
Taesung
T
D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D012044:Regression Analysis; D015398:Signal Transduction / Q000502:physiology*
D020543:Proteome