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start [2009/12/30 13:15]
aconesa
start [2010/05/03 16:51] (current)
jcarbonell
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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| ​
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