cross-platform microarray data normalisation for regulatory network inference跨平台的微阵列数据正常化监管网络推理.pdfVIP

Cross-Platform Microarray Data Normalisation for Regulatory Network Inference ˆ Alina Sırbu*, Heather J. Ruskin, Martin Crane Centre for Scientific Computing and Complex Systems Modelling, Dublin City University, Dublin, Ireland Abstract Background: Inferring Gene Regulatory Networks (GRNs) from time course microarray data suffers from the dimensionality problem created by the short length of available time series compared to the large number of genes in the network. To overcome this, data integration from diverse sources is mandatory. Microarray data from different sources and platforms are publicly available, but integration is not straightforward, due to platform and experimental differences. Methods: We analyse here different normalisation approaches for microarray data integration, in the context of reverse engineering of GRN quantitative models. We introduce two preprocessing approaches based on existing normalisation techniques and provide a comprehensive comparison of normalised datasets. Conclusions: Results identify a method based on a combination of Loess normalisation and iterative K-means as best for time series normalisation for this problem. ˆ Citation: Sırbu A, Ruskin HJ, Crane M (2010) Cross-Platform Microarray Data Normalisation for Regulatory Network Inference. PLoS ONE 5(11): e13822. doi:10.1371/journal.pone.0013822 Editor: Raya Khanin, Memorial Sloan-Kettering Cancer Center, United States of America Received June 9, 2010; Accepted October 18, 2010; Published November 12, 2010 ˆ Copyright: 2010 Sırbu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited