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A measurement error model for microarray data analysis

Progress in Natural Science:Materials International 2005年第7期15卷 614-620页

作者： ZHOU Yiming and CHENG Jing ( Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Beijing 102206, China) Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China State Key Laboratory of Biomembrane and Membrane Biotechnology Tsinghua University Beijing 100084 China National Engineering Research Center for Beijing Biochip Technology 18 Life Science Parkway Beijing 102206 China

Microarray technology has been widely used to analyze the gene expression levels by detecting fluorescence intensity in a high throughput fashion. However, since the measurement error produced from various sources in microarray experiments is heterogeneous and too large to be ignored, we propose here a measurement error model for microarray data processing, by which the standard deviation of the measurement error is demonstrated to be linearly increased with fluorescence intensity. A robust algorithm, which estimates the parameters of the measurement error model from a single microarray without replicated spots, is provided. The model and algorithm for estimating of the parameters from a given data set are tested on both the real data set and the simulated data set, and the result has been proven satisfactory. And, combining the measurement error model with traditional Z-test method, a full statistical model has been developed It can significantly improve the statistical inference for identifying differentially expressed genes.

关键词： microarray measurement error model parameter estimation differentially expressed genes.

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Profiling of differentially expressed genes.in ectomycorrhizal fungus Pisolithus tinctorius responding to Mycorrhiza Helper Brevibacillus reuszeri MPt17

Profiling of Differentially Expressed Genes in ectomycorrhiz...

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江苏省植物病理学会第十二次会员代表大会暨学术研讨会

作者： Ai-Dong Zhou Xiao-Qin Wu Jian-Ren Ye Lan Shen Xu-Ling Xu Lin Huang College of Forest Resources and Environment Nanjing Forestry University

Pisolithus tinctorius could form ectomycorrhiza with wide range of forest tree species,it has become a model organism to study ectomycorrhiza *** helper bacteria(MHB) are soil borne,directly involved in mycorrhiza formation and able to promote mycorrhizal ***,the molecular mechanisms of the interaction between *** and MHB are poorly *** our study,a eDNA library of the ECM fungus P tinctorius Pt2 after interaction with the MHB Brevibacillus reuszeri MPtl7 was constructed by suppression subtraction hybridization(SSH).Total RNA from *** MPtl7 exudates treated P tinctorius Pt2 was used as a "tester" and total RNA from non-bacterial treated P tinctorius Pt2 was used as a "driver." Among the differentially expressed sequences,a BLASTX in the NCBI non-redundant protein sequence database revealed that 75%of the nonredundant sequences(147 out of 196)were highly homologous to known proteins(E-value genes.were all up-regulated in the MPtl 7-treated *** results provide evidence that the MHB *** MPt17 could significantly change the expression of symbiosis-related genes.and genes.in mycelium development in P tinctorius Pt2,and also support the hypothesis that the MHB functions as helper though promotion on fungal mycelium.

关键词： mycorrhiza helper bacteria(MHB) Brevibacillus reuszeri MPt17 Pisolithus tinctorius Pt2 suppression subtraction hybridization(SSH) differentially expressed genes.

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