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| ====== Serial Expression Analysis ====== | ====== Serial Expression Analysis ====== | ||
| - | Serial Expression Analysis (SEA) is a web site for the analysis of serial gene expression data. Serial data is understood as multifactorial experimental designs where one of the factors is a quantitative variable such as time or treatment dose. The site offers five different methodologies for the identification of genes and functional classes which significant changes across series. | + | **S**erial **E**xpression **A**nalysis (**SEA**) is a web site for the analysis of serial gene expression data. Serial data is understood as multifactorial experimental designs where one of the factors is a quantitative variable such as time or treatment dose. The site offers five different methodologies for the identification of genes and functional classes which significant changes across series. \\ |
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| - | ===== References ===== | + | {{ :roadmap_low.png |}} |
| - | [1] Conesa, A.; Nueda, M.J.; Ferrer, A. and Talón, M. (2006) maSigPro: a Method to Identify Significantly Differential Expression Profiles in Time-Course Microarray Experiments. Bioinformatics, 22 (9), 1096-1102.\\ | + | |
| - | [2] Nueda, M.J.; Conesa, A.; Westerhuis, J.A.; Hoefsloot, H.C.J.; Smilde, A.K.; Talón, M. and Ferrer, A. (2007) Discovering gene expression patterns in Time Course Microarray Experiments by ANOVA-SCA. Bioinformatics, 23 (14), 1792-1800.\\ | + | |
| - | [3] Smilde, A.K.; Jansen, J.J.; Hoefsloot, H.C.J.; Lamers, R.J.A.N.; Van der Greef, J. and Timmerman, M.E. (2005) ANOVA-Simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data. Bioinformatics, 21 (13), 3043-3048. | + | |
| - | [4] Nueda, M.J.; Sebastián, P.; Tarazona, S.; García-García, F.; Dopazo, J.; Ferrer, A. and Conesa, A. (2009) Functional Assessment of Time Course Microarray data. BMC Bioinformatics. 10 (suppl 6): S9. | + | |
| + | The following table summarizes the main characteristics of the SEA algorithms:\\ | ||
| + | |**Name**|**Statistical Strategy**|**Selected Features** |**Selection criterion**| | ||
| + | |maSigPro|Univariate Regression|Genes| Genes with differential expression profiles| | ||
| + | |maSigFun| Univariate Regression| Functional Categories|Functional classes with most genes having correlated differential expression profiles| | ||
| + | |ASCA-genes|ANOVA + Multivariate Projection|Genes|Genes that follow major expression trends| | ||
| + | |ASCA-functional|ANOVA + Multivariate Projection + GSA|Functional Categories|Functional classes associated to a given expression trend| | ||
| + | |PCA-maSigFun|Multivariate Projection + Univariate Regression|Functional Categories| Functional classes with subset of genes showing correlated differential expression profiles| | ||
