Omics, integration

Thongboonkerd V. Genomics, proteomics and integrative omics in hypertension research. Curr Opin Nephrol Hypertens 2005 14 133-9. 

Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, et al. Next generation simulation tools the Systems Biology Workbench and BioSPICE integration. Omics 2003 7 355-72. 

Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, et al. Chemical Effects in Biological Systems—Data Dictionary (CEBS-DD) a compendium of terms for the capture and integration of biological study design description, conventional phenotypes and omics data. Toxicol Sci 2005 88 585-601. 

Herbert M Sauro, Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, and Hiroaki Kitano, Next generation simulation tools The systems biology workbench and BioSPICE integration. OMICS 7(4), 355 372 (2003). 

Several approaches are utilized to study systems biology. The bottom-up approach starts from the molecular level, the omics, to identify and evaluate the genomic and proteomic basis of diseases. The top-down approach attempts to integrate human physiology and diseases to provide models to understand disease pathways at organ levels. 

Omics Data Integration in Systems Biology Methods and Applications... 

Integrative Omics Analysis 446 Visualization of Omics Data 452 ... 

By integrative analysis of omics data, we understand the algorithmic and statistical approaches that pursue the combination of different omics data in one analysis. We can identify two major general strategies (24,54) ... 

FIGURE 1 Multivariate approaches for omics data integration. (A) The RV coefficient is a correlation measure between datasets that can be used as distance metric. (B) The 02PLS method dissects gene expression and metabolomics datasets for shared and data type-specific variation. (C) The N-way approach accommodates experimental factors in a multidimensional block. Tucker3 is used to study intradataset covariation and NPLS analyzes between-block covariation. Panel (B) Reproduced from Bylesjo et al. (23). Panel (C) Reproduced from Conesa et al. (24). 

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