Biclustering Of Gene Expression Data Research Articles

Maximal-Sum submatrix search using a hybrid contraint programming/linear programming approach

A Maximal-Sum Submatrix (MSS) maximizes the sum of the entries corresponding to the Cartesian product of a subset of rows and columns from an original matrix (with positive and negative entries). Despite being NP-hard, this recently introduced problem was already proven to be useful for practical data-mining applications. It was used for identifying bi-clusters in gene expression data or to extract a submatrix that is then visualized in a circular plot. The state-of-the-art results for MSS are obtained using an advanced Constraint Programing approach that combines a custom filtering algorithm with a Large Neighborhood Search. We improve the state-of-the-art approach by introducing new upper bounds based on linear and mixed-integer programming formulations, along with dedicated pruning algorithms. We experiment on both synthetic and real-life data, and show that our approach outperforms the previous methods.

Evolutionary Local Search Algorithm for the biclustering of gene expression data based on biological knowledge

Biclustering is an unsupervised classification technique that plays an increasingly important role in the study of modern biology. This data mining technique has provided answers to several challenges raised by the analysis of biological data and more particularly the analysis of gene expression data. It aims to cluster simultaneously genes and conditions. These unsupervised techniques are based essentially on the assumption that the extraction of the co-expressed genes allows to have co-regulated genes. In addition, the integration of biological information in the search process may induce to the extraction of relevant and non-trivial biclusters. Therefore, this work proposes an evolutionary algorithm based on local search method that relies on biological knowledge. An experimental study is achieved on real microarray datasets to evaluate the performance of the proposed algorithm. The assessment and the comparison are based on statistical and biological criteria. A cross-validation experiment is also used to estimate its accuracy. Promising results are obtained. They demonstrate the importance of the integration of the biological knowledge in the biclustering process to foster the efficiency and to promote the discovery of non-trivial and biologically relevant biclusters.

Non-swarm intelligence algorithms: a case study

The case study of plant intelligence inspired novel non-swarm intelligence (NSI) algorithms, namely Venus Flytrap Optimization and Bladder-Worts Suction, concentrated in this paper. These algorithms devised on the prey-hunting mechanisms of the Venus Flytrap (Dionaea Muscipula) and BladderWorts (Utricularia) plants, respectively. A comparative view of these algorithms is discussed. The main-support criterion is the major characteristic of these approaches. The benefits of this main-support criterion and their performances are evidenced with a case study of extracting the highly correlated maximal local patterns in gene expression data through biclustering. The NSI algorithms are proposed for biclustering gene expression data in this paper. The results are compared with existing optimization techniques like PSO and GA, and biclustering approaches like Cheng and Church, OPSM, BiMax, and Plaid approaches. This analysis evidenced the performance of NSI algorithms can yield optimal maximal local patterns with high correlation. Further, various real-time research applications of NSI approaches are also discussed.

Automatic evolution of bi-clusters from microarray data using self-organized multi-objective evolutionary algorithm

In the current paper, a novel approach is proposed for bi-clustering of gene expression data using the fusion of differential evolution framework and self-organizing map (SOM), named as BiClustSMEA. Variable number of gene and condition cluster centers are encoded in different solutions of the population to determine the number of bi-clusters from a dataset in an automated way. The concept of SOM is utilized in designing new genetic operators for both gene and condition clusters to reach to the optimal solution in a faster way. In order to measure the goodness of a bi-clustering solution, three bi-cluster quality measures, mean squared error, row variance, and bi-cluster size, are optimized simultaneously using differential evolution as the underlying optimization strategy. The concept of polynomial mutation is incorporated in our framework to generate highly diverse solutions which in turn helps in faster convergence. The proposed approach is applied on two real-life microarray gene expression datasets and results are compared with various state-of-the-art techniques. Results obtained clearly illustrate that our approach extracts high-quality bi-clusters as compared to other methods and also it converges much faster than other competitors. Further, the obtained results are validated using statistical significance test and biological significance test.

A novel biclustering of gene expression data based on hybrid BAFS-BSA algorithm

As one of usual concepts, co-expressed genes can represent co-regulated genes in gene expression data. This strategy can be refined further because co-expression of the genome may be the result of independent activation under same experimental samples, rather than the same regulatory regime. Therefore, traditional clustering techniques are proposed to find significant clusters, especially, the biclustering technology. By combining Binary Artificial Fish Swarm (BAFS) with Binary Simulated Annealing (BSA) algorithms, the hybrid algorithm named BAFS-BSA-BIC was proposed in this paper. When this method of biclustering was applied to several datasets, lots of biological significant bifclusters were searched, and the results demonstrate the promising clustering performance of our method. The proposed technology was also compared to classical biclustering technologies-CC, QUBIC, FLOC and original BAFS algorithm, and its robustness and quality are better than these algorithms in searching optimal biclusters of co-expressed genes.

The Use of Informed Priors in Biclustering of Gene Expression with the Hierarchical Dirichlet Process.

We motivate and describe the application of Hierarchical Dirichlet Process (HDP) models to the "soft" biclustering of gene expression data, in which we obtain modules (biclusters) where the affiliation of genes and samples with the modules are weighted, instead of being hard memberships. As a distinct contribution, we propose a method which HDP is informed with prior beliefs, significantly increasing the quality of the biclustering in terms of both the correctness of the number of modules inferred, and the precision of these modules, especially when evidence is sparse. We outline two such informed priors; one based on co-expression relationships inherent in the data, the other based on an externally provided regulatory network. We validate these results and compare the performance of our approach to Weighted Gene Correlation Network Analysis (WGCNA), another model that features weighted modules. We have, to this end, performed experiments on semi-synthetic data. The results show that HDP, with the addition of a well-informed prior, is able to capture the correct number of modules with increased accuracy. Furthermore, the model becomes robust to changes in the strength of the prior. We conclude by discussing these results and the benefits provided by our approach for gene expression analysis and network validation.

RN+: A Novel Biclustering Algorithm for Analysis of Gene Expression Data Using Protein-Protein Interaction Network.

Biclustering is a process of finding groups of genes that behave similarly under a subset of conditions. In this article, we propose an efficient biclustering algorithm, namely RN+, to identify biologically meaningful biclusters in gene expression data. The RN+ algorithm finds biologically meaningful biclusters through a novel gene filtering using protein-protein interaction network, gene searching, gene grouping, and queuing process. It also efficiently removes duplicate biclusters. We tested the proposed RN+ on five real microarray datasets, and compared its performance with seven competitive biclustering algorithms. The experimental results show that RN+ efficiently finds functionally enriched and biologically meaningful biclusters for large gene expression datasets, and outperforms the other tested biclustering algorithms on real datasets.

Biclustering of Gene Expression Data Using Cuckoo Search and Genetic Algorithm

Biclustering analysis of gene expression data can reveal a large number of biologically significant local gene expression patterns. Therefore, a large number of biclustering algorithms apply meta-heuristic algorithms such as genetic algorithm (GA) and cuckoo search (CS) to analyze the biclusters. However, different meta-heuristic algorithms have different applicability and characteristics. For example, the CS algorithm can obtain high-quality bicluster and strong global search ability, but its local search ability is relatively poor. In contrast to the CS algorithm, the GA has strong local search ability, but its global search ability is poor. In order to not only improve the global search ability of a bicluster and its coverage, but also improve the local search ability of the bicluster and its quality, this paper proposed a meta-heuristic algorithm based on GA and CS algorithm (GA-CS Biclustering, Georgia Association of Community Service Boards (GACSB)) to solve the problem of gene expression data clustering. The algorithm uses the CS algorithm as the main framework, and uses the tournament strategy and the elite retention strategy based on the GA to generate the next generation of the population. Compared with the experimental results of common biclustering analysis algorithms such as correlated correspondence (CC), fast, local clustering (FLOC), interior search algorithm (ISA), Securities Exchange Board of India (SEBI), sum of squares between (SSB) and coordinated scheduling/beamforming (CSB), the GACSB algorithm can not only obtain biclusters of high quality, but also obtain biclusters of high-biologic significance. In addition, we also use different bicluster evaluation indicators, such as Average Correlation Value (ACV), Mean-Squared Residue (MSR) and Virtual Error (VE), and verify that the GACSB algorithm has a strong scalability.

Runibic: a Bioconductor package for parallel row-based biclustering of gene expression data.

Biclustering is an unsupervised technique of simultaneous clustering of rows and columns of input matrix. With multiple biclustering algorithms proposed, UniBic remains one of the most accurate methods developed so far. In this paper we introduce a Bioconductor package called runibic with parallel implementation of UniBic. For the convenience the algorithm was reimplemented, parallelized and wrapped within an R package called runibic. The package includes: (i) a couple of times faster parallel version of the original sequential algorithm, (ii) much more efficient memory management, (iii) modularity which allows to build new methods on top of the provided one and (iv) integration with the modern Bioconductor packages such as SummarizedExperiment, ExpressionSet and biclust. The package is implemented in R and is available from Bioconductor (starting from version 3.6) at the following URL http://bioconductor.org/packages/runibic with installation instructions and tutorial. Supplementary data are available at Bioinformatics online.

A new FCA-based method for identifying biclusters in gene expression data

Biclustering has been very relevant within the field of gene expression data analysis. In fact, its main thrust stands in its ability to identify groups of genes that behave in the same way under a subset of samples (conditions). However, the pioneering algorithms of the literature has shown some limits in terms of the quality of unveiled biclusters. In this paper, we introduce a new algorithm, called BiFCA+, for biclustering microarray data. BiFCA+ heavily relies on the mathematical background of the formal concept analysis, in order to extract the set of biclusters. In addition, the Bond correlation measure is of use to filter out the overlapping biclusters. The extensive experiments, carried out on real-life datasets, shed light on BiFCA+’s ability to identify statistically and biologically significant biclusters.

Two-way learning with one-way supervision for gene expression data

BackgroundA family of parsimonious Gaussian mixture models for the biclustering of gene expression data is introduced. Biclustering is accommodated by adopting a mixture of factor analyzers model with a binary, row-stochastic factor loadings matrix. This particular form of factor loadings matrix results in a block-diagonal covariance matrix, which is a useful property in gene expression analyses, specifically in biomarker discovery scenarios where blood can potentially act as a surrogate tissue for other less accessible tissues. Prior knowledge of the factor loadings matrix is useful in this application and is reflected in the one-way supervised nature of the algorithm. Additionally, the factor loadings matrix can be assumed to be constant across all components because of the relationship desired between the various types of tissue samples. Parameter estimates are obtained through a variant of the expectation-maximization algorithm and the best-fitting model is selected using the Bayesian information criterion. The family of models is demonstrated using simulated data and two real microarray data sets. The first real data set is from a rat study that investigated the influence of diabetes on gene expression in different tissues. The second real data set is from a human transcriptomics study that focused on blood and immune tissues. The microarray data sets illustrate the biclustering family’s performance in biomarker discovery involving peripheral blood as surrogate biopsy material.ResultsThe simulation studies indicate that the algorithm identifies the correct biclusters, most optimally when the number of observation clusters is known. Moreover, the biclustering algorithm identified biclusters comprised of biologically meaningful data related to insulin resistance and immune function in the rat and human real data sets, respectively.ConclusionsInitial results using real data show that this biclustering technique provides a novel approach for biomarker discovery by enabling blood to be used as a surrogate for hard-to-obtain tissues.

Ensemble biclustering gene expression data based on the spectral clustering

Many biclustering algorithms and bicluster criteria have been proposed in analyzing the gene expression data. However, there are no clues about the choice of a specific biclustering algorithm, which make ensemble biclustering method receive much attention for aggregating the advantage of various biclustering algorithms. Although the method of co-association consensus (COAC) is a landmark of ensemble biclustering, the effectiveness and efficiency are the worst in state-of-the-art methods. In this paper, to improve COAC, we propose spectral ensemble biclustering (SEB) in which an novel method for generating a set of basic biclusters is proposed for generating the basic biclusters with better quality as well as higher diversity and an new consensus method is also adopted for combing the above basic biclusters. In SEB, spectral clustering is directly applied to the co-association matrix and equivalently transformed into the weighted k-means. Experiments on six gene expression data demonstrate that the effectiveness, efficiency and scalability of SEB are the best compared with existing ensemble methods in terms of the biological significance and runtime.

A Comparative Study of Clustering and Biclustering of Microarray Data

There are subsets of genes that have similar behavior under subsets of conditions, so we say that they coexpress, but behave independently under other subsets of conditions. Discovering such coexpressions can be helpful to uncover genomic knowledge such as gene networks or gene interactions. That is why, it is of utmost importance to make a simultaneous clustering of genes and conditions to identify clusters of genes that are coexpressed under clusters of conditions. This type of clustering is called biclustering. Biclustering is an NP-hard problem. Consequently, heuristic algorithms are typically used to approximate this problem by finding suboptimal solutions. In this paper, we make a new survey on clustering and biclustering of gene expression data, also called microarray data.

Fine-grained parallelization of fitness functions in bioinformatics optimization problems: gene selection for cancer classification and biclustering of gene expression data.

BackgroundMetaheuristics are widely used to solve large combinatorial optimization problems in bioinformatics because of the huge set of possible solutions. Two representative problems are gene selection for cancer classification and biclustering of gene expression data. In most cases, these metaheuristics, as well as other non-linear techniques, apply a fitness function to each possible solution with a size-limited population, and that step involves higher latencies than other parts of the algorithms, which is the reason why the execution time of the applications will mainly depend on the execution time of the fitness function. In addition, it is usual to find floating-point arithmetic formulations for the fitness functions. This way, a careful parallelization of these functions using the reconfigurable hardware technology will accelerate the computation, specially if they are applied in parallel to several solutions of the population.ResultsA fine-grained parallelization of two floating-point fitness functions of different complexities and features involved in biclustering of gene expression data and gene selection for cancer classification allowed for obtaining higher speedups and power-reduced computation with regard to usual microprocessors.ConclusionsThe results show better performances using reconfigurable hardware technology instead of usual microprocessors, in computing time and power consumption terms, not only because of the parallelization of the arithmetic operations, but also thanks to the concurrent fitness evaluation for several individuals of the population in the metaheuristic. This is a good basis for building accelerated and low-energy solutions for intensive computing scenarios.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1200-9) contains supplementary material, which is available to authorized users.

Biclustering of human cancer microarray data using co-similarity based co-clustering

Biclustering of gene expression data aims at finding localized patterns in a subspace. A bicluster (sometimes called a co-cluster), in the context of gene expression data, is a set of genes that exhibit similar expression intensity under a subset of experimental features (conditions). Most biclustering algorithms proposed in the literature aim at finding sub-matrices that exhibit some sort of coherence by selecting an initial sub-matrix and iteratively adding or subtracting rows and columns. These algorithms are generally dependent on the initial, hard selection of the gene and condition clusters respectively. In this work, we adapt a recently proposed approach for clustering textual data to find biclusters in gene expression data. Our proposed technique is based on the concept of co-similarity between genes (and between conditions) that exploits weighted higher order paths in a bipartite graph representation of the gene expression data. Therefore, we build statistical relations between genes and between conditions by comparing all genes and conditions before finally extracting biclusters from the data. We show that the proposed technique is able to find meaningful non-overlapping biclusters both on synthetically generated data as well as real cancer data. Our results indicate that the proposed technique is resistant to noise in the data and can successfully retrieve biclusters even in the presence of relatively large amount of noise. We also analyze our results with respect to the discovered genes and observe that our extracted biclusters are supported by biological evidences, such as enrichment of gene functions and biological processes.

A Meta-Heuristic Approach for Discovering Local Pattern in Gene Expression Data

The biclustering of gene expression data is an important technology for biologists. Biclustering is used to discover groups of genes that are co-expressed over a subset of conditions in microarray gene expression data. There has been a lot of research in biclustering involving statistical and graph-theoretic approach. This entails that an exhaustive search of the space of solutions may be infeasible and problem is NP-hard. Hence metaheuristic approach, the Harmony Search (HS) method finds the coherent biclusters in large expression data. The experiment results are demonstrated on two benchmark datasets. Furthermore, we also test the ability of HS method to locate biologically verifiable biclusters within an annotated set of genes.

Evaluation of Plaid Models in Biclustering of Gene Expression Data.

Background. Biclustering algorithms for the analysis of high-dimensional gene expression data were proposed. Among them, the plaid model is arguably one of the most flexible biclustering models up to now. Objective. The main goal of this study is to provide an evaluation of plaid models. To that end, we will investigate this model on both simulation data and real gene expression datasets. Methods. Two simulated matrices with different degrees of overlap and noise are generated and then the intrinsic structure of these data is compared with biclusters result. Also, we have searched biologically significant discovered biclusters by GO analysis. Results. When there is no noise the algorithm almost discovered all of the biclusters but when there is moderate noise in the dataset, this algorithm cannot perform very well in finding overlapping biclusters and if noise is big, the result of biclustering is not reliable. Conclusion. The plaid model needs to be modified because when there is a moderate or big noise in the data, it cannot find good biclusters. This is a statistical model and is a quite flexible one. In summary, in order to reduce the errors, model can be manipulated and distribution of error can be changed.

Nanoinformatics for environmental health and biomedicine.

Nanoinformatics for environmental health and biomedicine.

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials.

Background: The presence of diverse types of nanomaterials (NMs) in commerce is growing at an exponential pace. As a result, human exposure to these materials in the environment is inevitable, necessitating the need for rapid and reliable toxicity testing methods to accurately assess the potential hazards associated with NMs. In this study, we applied biclustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related biclusters of genes showing similar expression profiles were identified. The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO2), carbon black (CB) or carbon nanotubes (CNTs) to determine the disease significance of these data-driven gene sets.Results: Biclusters representing inflammation (chemokine activity), DNA binding, cell cycle, apoptosis, reactive oxygen species (ROS) and fibrosis processes were identified. All of the NM studies were significant with respect to the bicluster related to chemokine activity (DAVID; FDR p-value = 0.032). The bicluster related to pulmonary fibrosis was enriched in studies where toxicity induced by CNT and CB studies was investigated, suggesting the potential for these materials to induce lung fibrosis. The pro-fibrogenic potential of CNTs is well established. Although CB has not been shown to induce fibrosis, it induces stronger inflammatory, oxidative stress and DNA damage responses than nano-TiO2 particles.Conclusion: The results of the analysis correctly identified all NMs to be inflammogenic and only CB and CNTs as potentially fibrogenic. In addition to identifying several previously defined, functionally relevant gene sets, the present study also identified two novel genes sets: a gene set associated with pulmonary fibrosis and a gene set associated with ROS, underlining the advantage of using a data-driven approach to identify novel, functionally related gene sets. The results can be used in future gene set enrichment analysis studies involving NMs or as features for clustering and classifying NMs of diverse properties.

On Evolutionary Algorithms for Biclustering of Gene Expression Data

On Evolutionary Algorithms for Biclustering of Gene Expression Data