Omics’ data

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. 

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). 

Integrated visualization of different omics data types is probably the most powerful tool for the interpretation of SB results. While mathematical models... 

The MAGE has built within it a controlled vocabulary that is used to standardize communication between data providers. However, MAGE can also be extended to encode other types of omic data beyond genomics, such as proteomic data, so long as a reference to the ontology or controlled vocabulary is provided. Although a description of the extension mechanism is beyond scope of this book, practitioners must become familiar with it in order to ensure their software products and applications will be able to accept any and all annotation data that may be submitted with the genomic data. 

BL-SOM Platform for Riken Metabolomics An integrated analytical tool for a range of omics data (http //prime.psc.rikcn.jp/ action=blsom indcx)... 

Borgert CJ. 2007. Predicting interactions from mechanistic information can omic data validate theories Toxicol Appl Pharmacol 223 114—120. 

Additionally, genome-scale metabolic models (GSMMs) provide a framework for organizing, integrating, and analyzing omics data. A figure showing the basic steps and a simplified workflow [14,110] for reconstruction of metabolic models is shown in Fig. 2. 

Joyce, A.R. and Palsson, B.O. (2006) The model organism as a system integrating omics data sets. Nat. Rev. Mol. Cell Biol. 7,198-210. 

INTEGRATIVE PATHWAY AND NETWORK ANALYSIS FOR OMICS DATA... 

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