Gene expression data

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Computational methods have been applied to determine the connections in systems that are not well-defined by canonical pathways. This is either done by semi-automated and/or curated literature causal modeling [1] or by statistical methods based on large-scale data from expression or proteomic studies (a mostly theoretical approach is given by reference [2] and a more applied approach is in reference [3]). Many methods, including clustering, Bayesian analysis and principal component analysis have been used to find relationships and "fingerprints" in gene expression data [4]. 

DrugMatrix Iconix Pharmaceuticals, Inc. [http // www.iconixpharma.com/] Pharmacology data integrated with extensive gene expression data... 

That there are many different effects of toxicants aside from changes in gene expression, such as effects on membrane integrity, and these effects might not be extrapolated from single endpoint gene expression data. 

Exploiting Public Databases and Repositories of Gene Expression Data... 

To use analysis tools to organize the gene expression data (gene expression profihng) in a way that will... 

Verification of Gene Expression Data Using RT-PCR (Optional)... 

If verification of gene expression data from the array analyses is desired, this can be performed according to a method presented elsewhere (14). 

Pounds S, Cheng C (2005) Statistical development and evaluation of microarray gene expression data filters. J Comput Biol 12 482-495. doi 10.1089/cmb.2005.12.482... 

Wen Z et al (2010) Evaluation of gene expression data generated firom expired Affymettix GeneChip(R) microarrays using MAQC reference BNA samples. BMC Bioinformatics ll(Suppl 6) S10. doi 1471-2105-ll-S6-S10 (pii)10.1186/1471-2105-ll-S6-S10... 

Qin LX, Self SG (2006) The clustering of regression models method with applications in gene expression data. Biometrics 62 526-533. doi BIOM498 (pii)lO.llll/ j.l541-0420.2005.00498.x... 

Chen YJ et al (2003) Normalization methods for analysis of microarray gene-expression data. J Biopharm Stat 13 57-74... 

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