Stefan Bleuler

Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes

The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation.

A systematic comparison and evaluation of biclustering methods for gene expression data

MOTIVATION In recent years, there have been various efforts to overcome the limitations of standard clustering approaches for the analysis of gene expression data by grouping genes and samples simultaneously. The underlying concept, which is often referred to as biclustering, allows to identify sets of genes sharing compatible expression patterns across subsets of samples, and its usefulness has been demonstrated for different organisms and datasets. Several biclustering methods have been proposed in the literature; however, it is not clear how the different techniques compare with each other with respect to the biological relevance of the clusters as well as with other characteristics such as robustness and sensitivity to noise. Accordingly, no guidelines concerning the choice of the biclustering method are currently available. RESULTS First, this paper provides a methodology for comparing and validating biclustering methods that includes a simple binary reference model. Although this model captures the essential features of most biclustering approaches, it is still simple enough to exactly determine all optimal groupings; to this end, we propose a fast divide-and-conquer algorithm (Bimax). Second, we evaluate the performance of five salient biclustering algorithms together with the reference model and a hierarchical clustering method on various synthetic and real datasets for Saccharomyces cerevisiae and Arabidopsis thaliana. The comparison reveals that (1) biclustering in general has advantages over a conventional hierarchical clustering approach, (2) there are considerable performance differences between the tested methods and (3) already the simple reference model delivers relevant patterns within all considered settings.

A Tutorial on Evolutionary Multiobjective Optimization

Multiple, often conflicting objectives arise naturally in most real-world optimization scenarios. As evolutionary algorithms possess several characteristics that are desirable for this type of problem, this class of search strategies has been used for multiobjective optimization for more than a decade. Meanwhile evolutionary multiobjective optimization has become established as a separate subdiscipline combining the fields of evolutionary computation and classical multiple criteria decision making.

PISA: a platform and programming language independent interface for search algorithms

This paper introduces an interface specification (PISA) that allows to separate the problem-specific part of an optimizer from the problem-independent part. We propose a view of the general optimization scenario, where the problem representation together with the variation operators is seen as an integral part of the optimization problem and can hence be easily separated from the selection operators. Both parts are implemented as independent programs, that can be provided as ready-to-use packages and arbitrarily combined. This makes it possible to specify and implement representation-independent selection modules, which form the essence of modern multiobjective optimization algorithms. The variation operators, on the other hand, have to be defined in one module together with the optimization problem, facilitating a customized problem description. Besides the specification, the paper contains a correctness proof for the protocol and measured efficiency results.

Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana

We present a novel graphical Gaussian modeling approach for reverse engineering of genetic regulatory networks with many genes and few observations. When applying our approach to infer a gene network for isoprenoid biosynthesis in Arabidopsis thaliana, we detect modules of closely connected genes and candidate genes for possible cross-talk between the isoprenoid pathways. Genes of downstream pathways also fit well into the network. We evaluate our approach in a simulation study and using the yeast galactose network.

BicAT: a biclustering analysis toolbox

SUMMARY Besides classical clustering methods such as hierarchical clustering, in recent years biclustering has become a popular approach to analyze biological data sets, e.g. gene expression data. The Biclustering Analysis Toolbox (BicAT) is a software platform for clustering-based data analysis that integrates various biclustering and clustering techniques in terms of a common graphical user interface. Furthermore, BicAT provides different facilities for data preparation, inspection and postprocessing such as discretization, filtering of biclusters according to specific criteria or gene pair analysis for constructing gene interconnection graphs. The possibility to use different biclustering algorithms inside a single graphical tool allows the user to compare clustering results and choose the algorithm that best fits a specific biological scenario. The toolbox is described in the context of gene expression analysis, but is also applicable to other types of data, e.g. data from proteomics or synthetic lethal experiments. AVAILABILITY The BicAT toolbox is freely available at http://www.tik.ee.ethz.ch/sop/bicat and runs on all operating systems. The Java source code of the program and a developers guide is provided on the website as well. Therefore, users may modify the program and add further algorithms or extensions.

RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization

BackgroundRT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls. There is increasing evidence, however, that the expression of commonly used reference genes can vary significantly in certain contexts.ResultsUsing the Genevestigator database of normalized and well-annotated microarray experiments, we describe the expression stability characteristics of the transciptomes of several organisms. The results show that a) no genes are universally stable, b) most commonly used reference genes yield very high transcript abundances as compared to the entire transcriptome, and c) for each biological context a subset of stable genes exists that has smaller variance than commonly used reference genes or genes that were selected for their stability across all conditions.ConclusionWe therefore propose the normalization of RT-qPCR data using reference genes that are specifically chosen for the conditions under study. RefGenes is a community tool developed for that purpose. Validation RT-qPCR experiments across several organisms showed that the candidates proposed by RefGenes generally outperformed commonly used reference genes. RefGenes is available within Genevestigator at http://www.genevestigator.com.

Multiobjective genetic programming: reducing bloat using SPEA2

This study investigates the use of multiobjective techniques in genetic programming (GP) in order to evolve compact programs and to reduce the effects caused by bloating. The proposed approach considers the program size as a second, independent objective besides the program functionality. In combination with a multiobjective evolutionary technique, SPEA2, this method outperforms four other strategies to reduce bloat with regard to both convergence speed and size of the produced programs on an even-parity problem.

An EA framework for biclustering of gene expression data

In recent years, several biclustering methods have been suggested to identify local patterns in gene expression data. Most of these algorithms represent greedy strategies that are heuristic in nature: an approximate solutions is found within reasonable time bounds. The quality of biclustering, though, is often considered more important than the computation time required to generate it. Therefore, this paper addresses the question whether additional run-time resources can be exploited in order to improve the outcome of the aforementioned greedy algorithms. To this end, we propose a general framework that embed such biclustering methods as local search procedures in an evolutionary algorithm. We demonstrate on one prominent example that this approach achieves significant improvements in the quality of the biclusters when compared to the application of the greedy strategy alone.

Genevestigator Transcriptome Meta-Analysis and Biomarker Search using Rice and Barley Gene Expression Databases

The wide-spread use of microarray technologies to study plant transcriptomes has led to important discoveries and to an accumulation of profiling data covering a wide range of different tissues, developmental stages, perturbations, and genotypes. Querying a large number of microarray experiments can provide insights that cannot be gained by analyzing single experiments. However, such a meta-analysis poses significant challenges with respect to data comparability and normalization, systematic sample annotation, and analysis tools. Genevestigator addresses these issues using a large curated expression database and a set of specifically developed analysis tools that are accessible over the internet. This combination has already proven to be useful in the area of plant research based on a large set of Arabidopsis data (Grennan, 2006). Here, we present the release of the Genevestigator rice and barley gene expression databases that contain quality-controlled and well annotated microarray experiments using ontologies. The databases currently comprise experiments from pathology, plant nutrition, abiotic stress, hormone treatment, genotype, and spatial or temporal analysis, but are expected to cover a broad variety of research areas as more experimental data become available. The transcriptome meta-analysis of the model species rice and barley is expected to deliver results that can be used for functional genomics and biotechnological applications in cereals.