Group-wise ANOVA simultaneous component analysis for designed <Emphasis Type="Italic">omics</Emphasis> experiments

Introduction

Modern omics experiments pertain not only to the measurement of many variables but also follow complex experimental designs where many factors are manipulated at the same time. This data can be conveniently analyzed using multivariate tools like ANOVA-simultaneous component analysis (ASCA) which allows interpretation of the variation induced by the different factors in a principal component analysis fashion. However, while in general only a subset of the measured variables may be related to the problem studied, all variables contribute to the final model and this may hamper interpretation.

Objectives

We introduce here a sparse implementation of ASCA termed group-wise ANOVA-simultaneous component analysis (GASCA) with the aim of obtaining models that are easier to interpret.

Methods

GASCA is based on the concept of group-wise sparsity introduced in group-wise principal components analysis where structure to impose sparsity is defined in terms of groups of correlated variables found in the correlation matrices calculated from the effect matrices.

Results

The GASCA model, containing only selected subsets of the original variables, is easier to interpret and describes relevant biological processes.

Conclusions

GASCA is applicable to any kind of omics data obtained through designed experiments such as, but not limited to, metabolomic, proteomic and gene expression data.

     

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Some coprophilous fungi from Kenya

The occurrence of coprophilous fungi on samples of antelope, buffalo, zebra and hippopotamus dung collected from the Marula Estates in Kenya was recorded. A hundred and seventy three fungal isolates representative of 40 genera and 59 species were identified. Among these species, 23 were Ascomycetes (39%), 30 Deuteromycetes (50.8%), 5 Zygomycetes (8.5%) and 1 Basidiomycete (1.7%). Ascobolus immersus, Coprotus niveus, Iodophanus carneus, Lasiobolus lasioboloides, Podospora anserina, P. australis and Sporormiella minima were the dominant species occurring in the dung of these animals. Notes on infrequent or interesting Ascomycetes include Kernia nitida, Saccobolus versicolor, Sordaria fimicola and others. The interdependence of the vegetation of this area with the fungi occurring on the dung of these animals is discussed. This revised version was published online in June 2006 with corrections to the Cover Date.     

The role of alien fish (the centrarchid Micropterus salmoides) in lake food webs highlighted by stable isotope analysis

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