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Huang Y, Liu J, Zhu X. Mutations in lysine methyltransferase 2C and PEG3 are associated with tumor mutation burden, prognosis, and antitumor immunity in pancreatic adenocarcinoma patients. Digit Health 2022; 8:20552076221133699. [PMID: 36312851 PMCID: PMC9597037 DOI: 10.1177/20552076221133699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND As a common cancer-related death worldwide, pancreatic adenocarcinoma (PAAD) has significantly increased mortality in recent years. In recent years, tumor mutation burden (TMB) has been regarded as the most popular biomarker for PAAD immunotherapy. However, it remains unclear which gene mutations affect TMB and immune response in pancreatic adenocarcinoma. METHODS The somatic mutation images of PAAD samples were downloaded from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Based on the expression data of the TCGA and IGCC cohorts, various bioinformatics algorithms are used for evaluating the prognostic value and functional annotation of some frequently somatically mutated genes. Furthermore, the correlation between gene mutation and tumor immunity was also evaluated. RESULTS The results showed that lysine methyltransferase 2C (KMT2C) and paternally expressed 3 (PEG3) are frequently mutated genes in PAAD. Patients with KMT2C and PEG3 mutations have higher TMB severity and a lousy prognosis. In addition, the mutations of KMT2C and PEG3 genes positively regulate the metabolic and protein-related pathways in PAAD. Meanwhile, significant differences in the composition of the immune cells were observed for KMT2C and PEG3 mutations PAAD patients, for providing additional guidelines for antitumor treatments in various KMT2C and PEG3 mutation states in PAAD. CONCLUSION This study reveals that KMT2C and PEG3 mutation may serve as biomarkers for predicting prognosis and guiding anti-PAAD immunotherapy for PAAD patients.
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Affiliation(s)
- Yili Huang
- The Third Clinical Medical College, Henan University of Traditional Chinese
Medicine, Zhengzhou, Henan Province, People's Republic of China,Department of Radiotherapy, Henan Cancer Hospital, Zhengzhou, Henan Province, People's Republic of China,Xiaole Zhu, Pancreas Center, Jiangsu Province Hospital, 300
Guangzhou Road, Nanjing 210029, Jiangsu Province, People's Republic of China.
Jinsong Liu, Department of
Radiotherapy, Henan Cancer Hospital, 127 Dongming Road, Zhengzhou 450003, Henan
Province, People's Republic of China.
| | - Jinsong Liu
- The Third Clinical Medical College, Henan University of Traditional Chinese
Medicine, Zhengzhou, Henan Province, People's Republic of China,Department of Radiotherapy, Henan Cancer Hospital, Zhengzhou, Henan Province, People's Republic of China
| | - Xiaole Zhu
- Pancreas Center, Jiangsu Province Hospital,
Nanjing, Jiangsu Province, People's Republic of China
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Mandal K, Sarmah R, Bhattacharyya DK. POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2659-2670. [PMID: 32175872 DOI: 10.1109/tcbb.2020.2980816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To understand the underlying biological mechanisms of gene expression data, it is important to discover the groups of genes that have similar expression patterns under certain subsets of conditions. Biclustering algorithms have been effective in analyzing large-scale gene expression data. Recently, traditional biclustering has been improved by introducing biological knowledge along with the expression data during the biclustering process. In this paper, we propose the Pathway-based Order Preserving Biclustering (POPBic) algorithm by incorporating Kyoto Encyclopedia of Genes and Genomes (KEGG) based on the hypothesis that two genes sharing similar pathways are likely to be similar. The basic principle of the POPBic approach is to apply the concept of Longest Common Subsequence between a pair of genes which have a high number of common pathways. The algorithm identifies the expression patterns from data using two major steps: (i) selection of significant seed genes and (ii) extraction of biclusters. We performe exhaustive experimentation with the POPBic algorithm using synthetic dataset to evaluate the bicluster model, finding its robustness in the presence of noise and identifying overlapping biclusters. We demonstrate that POPBic is able to discover biologically significant biclusters for four cancer microarray gene expression datasets. POPBic has been found to perform consistently well in comparison to its closest competitors.
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Biological knowledge-slanted random forest approach for the classification of calcified aortic valve stenosis. BioData Min 2021; 14:35. [PMID: 34301292 PMCID: PMC8305490 DOI: 10.1186/s13040-021-00269-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/18/2021] [Indexed: 11/29/2022] Open
Abstract
Background Calcific aortic valve stenosis (CAVS) is a fatal disease and there is no pharmacological treatment to prevent the progression of CAVS. This study aims to identify genes potentially implicated with CAVS in patients with congenital bicuspid aortic valve (BAV) and tricuspid aortic valve (TAV) in comparison with patients having normal valves, using a knowledge-slanted random forest (RF). Results This study implemented a knowledge-slanted random forest (RF) using information extracted from a protein-protein interactions network to rank genes in order to modify their selection probability to draw the candidate split-variables. A total of 15,191 genes were assessed in 19 valves with CAVS (BAV, n = 10; TAV, n = 9) and 8 normal valves. The performance of the model was evaluated using accuracy, sensitivity, and specificity to discriminate cases with CAVS. A comparison with conventional RF was also performed. The performance of this proposed approach reported improved accuracy in comparison with conventional RF to classify cases separately with BAV and TAV (Slanted RF: 59.3% versus 40.7%). When patients with BAV and TAV were grouped against patients with normal valves, the addition of prior biological information was not relevant with an accuracy of 92.6%. Conclusion The knowledge-slanted RF approach reflected prior biological knowledge, leading to better precision in distinguishing between cases with BAV, TAV, and normal valves. The results of this study suggest that the integration of biological knowledge can be useful during difficult classification tasks. Supplementary Information The online version contains supplementary material available at 10.1186/s13040-021-00269-4.
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Maâtouk O, Ayadi W, Bouziri H, Duval B. Evolutionary Local Search Algorithm for the biclustering of gene expression data based on biological knowledge. Appl Soft Comput 2021. [DOI: 10.1016/j.asoc.2021.107177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Nepomuceno-Chamorro IA, Nepomuceno JA, Galván-Rojas JL, Vega-Márquez B, Rubio-Escudero C. Using prior knowledge in the inference of gene association networks. APPL INTELL 2020. [DOI: 10.1007/s10489-020-01705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Maâtouk O, Ayadi W, Bouziri H, Duval B. Evolutionary biclustering algorithms: an experimental study on microarray data. Soft comput 2019. [DOI: 10.1007/s00500-018-3394-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cesari G, Algaba E, Moretti S, Nepomuceno JA. An application of the Shapley value to the analysis of co-expression networks. APPLIED NETWORK SCIENCE 2018; 3:35. [PMID: 30839839 PMCID: PMC6214322 DOI: 10.1007/s41109-018-0095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/14/2018] [Indexed: 06/09/2023]
Abstract
We study the problem of identifying relevant genes in a co-expression network using a (cooperative) game theoretic approach. The Shapley value of a cooperative game is used to asses the relevance of each gene in interaction with the others, and to stress the role of nodes in the periphery of a co-expression network for the regulation of complex biological pathways of interest. An application of the method to the analysis of gene expression data from microarrays is presented, as well as a comparison with classical centrality indices. Finally, making further assumptions about the a priori importance of genes, we combine the game theoretic model with other techniques from cluster analysis.
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Affiliation(s)
- Giulia Cesari
- Department of Mathematics, Politecnico di Milano, Milano, Italy
| | - Encarnación Algaba
- Department of Applied Mathematics and IMUS, University of Seville, Seville, Spain
| | - Stefano Moretti
- Université Paris-Dauphine, PSL Research University, CNRS, LAMSADE, Paris, 75016 France
| | - Juan A. Nepomuceno
- Department of Computer Languages and Systems, University of Seville, Seville, Spain
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Parraga-Alava J, Dorn M, Inostroza-Ponta M. A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies. BioData Min 2018; 11:16. [PMID: 30100924 PMCID: PMC6081857 DOI: 10.1186/s13040-018-0178-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/29/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information about the behaviour of genetic information on different conditions. In order to analyse this data, clustering arises as one of the main techniques used, and it aims at finding groups of genes that have some criterion in common, like similar expression profile. However, the problem of finding groups is normally multi dimensional, making necessary to approach the clustering as a multi-objective problem where various cluster validity indexes are simultaneously optimised. They are usually based on criteria like compactness and separation, which may not be sufficient since they can not guarantee the generation of clusters that have both similar expression patterns and biological coherence. METHOD We propose a Multi-Objective Clustering algorithm Guided by a-Priori Biological Knowledge (MOC-GaPBK) to find clusters of genes with high levels of co-expression, biological coherence, and also good compactness and separation. Cluster quality indexes are used to optimise simultaneously gene relationships at expression level and biological functionality. Our proposal also includes intensification and diversification strategies to improve the search process. RESULTS The effectiveness of the proposed algorithm is demonstrated on four publicly available datasets. Comparative studies of the use of different objective functions and other widely used microarray clustering techniques are reported. Statistical, visual and biological significance tests are carried out to show the superiority of the proposed algorithm. CONCLUSIONS Integrating a-priori biological knowledge into a multi-objective approach and using intensification and diversification strategies allow the proposed algorithm to find solutions with higher quality than other microarray clustering techniques available in the literature in terms of co-expression, biological coherence, compactness and separation.
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Affiliation(s)
- Jorge Parraga-Alava
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Av. Ecuador 3659, Santiago, Chile
- Carrera de Computación, Escuela Superior Politécnica Agropecuaria de Manabí Manuel Félix López, Campus Politécnico Sitio El Limón, Calceta, Ecuador
| | - Marcio Dorn
- Instituto de Informatica, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, 91501-970 Brasil
| | - Mario Inostroza-Ponta
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Av. Ecuador 3659, Santiago, Chile
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Nepomuceno JA, Troncoso A, Nepomuceno-Chamorro IA, Aguilar-Ruiz JS. Pairwise gene GO-based measures for biclustering of high-dimensional expression data. BioData Min 2018; 11:4. [PMID: 29610579 PMCID: PMC5872503 DOI: 10.1186/s13040-018-0165-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/01/2018] [Indexed: 11/15/2022] Open
Abstract
Background Biclustering algorithms search for groups of genes that share the same behavior under a subset of samples in gene expression data. Nowadays, the biological knowledge available in public repositories can be used to drive these algorithms to find biclusters composed of groups of genes functionally coherent. On the other hand, a distance among genes can be defined according to their information stored in Gene Ontology (GO). Gene pairwise GO semantic similarity measures report a value for each pair of genes which establishes their functional similarity. A scatter search-based algorithm that optimizes a merit function that integrates GO information is studied in this paper. This merit function uses a term that addresses the information through a GO measure. Results The effect of two possible different gene pairwise GO measures on the performance of the algorithm is analyzed. Firstly, three well known yeast datasets with approximately one thousand of genes are studied. Secondly, a group of human datasets related to clinical data of cancer is also explored by the algorithm. Most of these data are high-dimensional datasets composed of a huge number of genes. The resultant biclusters reveal groups of genes linked by a same functionality when the search procedure is driven by one of the proposed GO measures. Furthermore, a qualitative biological study of a group of biclusters show their relevance from a cancer disease perspective. Conclusions It can be concluded that the integration of biological information improves the performance of the biclustering process. The two different GO measures studied show an improvement in the results obtained for the yeast dataset. However, if datasets are composed of a huge number of genes, only one of them really improves the algorithm performance. This second case constitutes a clear option to explore interesting datasets from a clinical point of view.
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Affiliation(s)
- Juan A Nepomuceno
- 1Departamento de Lenguajes y Sistemas Informáticos, Universidad de Sevilla, Avd. Reina Mercedes s/n, Seville, 41012 Spain
| | - Alicia Troncoso
- 2Área de Informática, Universidad Pablo de Olavide, Ctra. Utrera km. 1, Seville, 41013 Spain
| | - Isabel A Nepomuceno-Chamorro
- 1Departamento de Lenguajes y Sistemas Informáticos, Universidad de Sevilla, Avd. Reina Mercedes s/n, Seville, 41012 Spain
| | - Jesús S Aguilar-Ruiz
- 2Área de Informática, Universidad Pablo de Olavide, Ctra. Utrera km. 1, Seville, 41013 Spain
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Houari A, Ayadi W, Ben Yahia S. A new FCA-based method for identifying biclusters in gene expression data. INT J MACH LEARN CYB 2018. [DOI: 10.1007/s13042-018-0794-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Bentham RB, Bryson K, Szabadkai G. MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. Nucleic Acids Res 2017; 45:8712-8730. [PMID: 28911113 PMCID: PMC5587796 DOI: 10.1093/nar/gkx590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 07/01/2017] [Indexed: 12/16/2022] Open
Abstract
The potential to understand fundamental biological processes from gene expression data has grown in parallel with the recent explosion of the size of data collections. However, to exploit this potential, novel analytical methods are required, capable of discovering large co-regulated gene networks. We found current methods limited in the size of correlated gene sets they could discover within biologically heterogeneous data collections, hampering the identification of multi-gene controlled fundamental cellular processes such as energy metabolism, organelle biogenesis and stress responses. Here we describe a novel biclustering algorithm called Massively Correlated Biclustering (MCbiclust) that selects samples and genes from large datasets with maximal correlated gene expression, allowing regulation of complex networks to be examined. The method has been evaluated using synthetic data and applied to large bacterial and cancer cell datasets. We show that the large biclusters discovered, so far elusive to identification by existing techniques, are biologically relevant and thus MCbiclust has great potential in the analysis of transcriptomics data to identify large-scale unknown effects hidden within the data. The identified massive biclusters can be used to develop improved transcriptomics based diagnosis tools for diseases caused by altered gene expression, or used for further network analysis to understand genotype-phenotype correlations.
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Affiliation(s)
- Robert B Bentham
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London WC1E 6BT, UK.,The Francis Crick Institute, London NW1 1AT, UK
| | - Kevin Bryson
- Department of Computer Sciences, University College London, London WC1E 6BT, UK
| | - Gyorgy Szabadkai
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London WC1E 6BT, UK.,The Francis Crick Institute, London NW1 1AT, UK.,Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
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Paul AK, Shill PC. Incorporating gene ontology into fuzzy relational clustering of microarray gene expression data. Biosystems 2017; 163:1-10. [PMID: 29113811 DOI: 10.1016/j.biosystems.2017.09.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 12/28/2022]
Abstract
The product of gene expression works together in the cell for each living organism in order to achieve different biological processes. Many proteins are involved in different roles depending on the environment of the organism for the functioning of the cell. In this paper, we propose gene ontology (GO) annotations based semi-supervised clustering algorithm called GO fuzzy relational clustering (GO-FRC) where one gene is allowed to be assigned to multiple clusters which are the most biologically relevant behavior of genes. In the clustering process, GO-FRC utilizes useful biological knowledge which is available in the form of a gene ontology, as a prior knowledge along with the gene expression data. The prior knowledge helps to improve the coherence of the groups concerning the knowledge field. The proposed GO-FRC has been tested on the two yeast (Saccharomyces cerevisiae) expression profiles datasets (Eisen and Dream5 yeast datasets) and compared with other state-of-the-art clustering algorithms. Experimental results imply that GO-FRC is able to produce more biologically relevant clusters with the use of the small amount of GO annotations.
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Affiliation(s)
- Animesh Kumar Paul
- Department of Computer Science and Engineering, Khulna University of Engineering & Technology, Khulna, Bangladesh.
| | - Pintu Chandra Shill
- Department of Computer Science and Engineering, Khulna University of Engineering & Technology, Khulna, Bangladesh
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Kléma J, Malinka F, Železný F. Semantic biclustering for finding local, interpretable and predictive expression patterns. BMC Genomics 2017. [PMID: 29513193 PMCID: PMC5657082 DOI: 10.1186/s12864-017-4132-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background One of the major challenges in the analysis of gene expression data is to identify local patterns composed of genes showing coherent expression across subsets of experimental conditions. Such patterns may provide an understanding of underlying biological processes related to these conditions. This understanding can further be improved by providing concise characterizations of the genes and situations delimiting the pattern. Results We propose a method called semantic biclustering with the aim to detect interpretable rectangular patterns in binary data matrices. As usual in biclustering, we seek homogeneous submatrices, however, we also require that the included elements can be jointly described in terms of semantic annotations pertaining to both rows (genes) and columns (samples). To find such interpretable biclusters, we explore two strategies. The first endows an existing biclustering algorithm with the semantic ingredients. The other is based on rule and tree learning known from machine learning. Conclusions The two alternatives are tested in experiments with two Drosophila melanogaster gene expression datasets. Both strategies are shown to detect sets of compact biclusters with semantic descriptions that also remain largely valid for unseen (testing) data. This desirable generalization aspect is more emphasized in the strategy stemming from conventional biclustering although this is traded off by the complexity of the descriptions (number of ontology terms employed), which, on the other hand, is lower for the alternative strategy.
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Affiliation(s)
- Jiří Kléma
- Department of Computer Science, Czech Technical University in Prague, Karlovo náměstí 13, 121 35, Prague 2, Czech Republic.
| | - František Malinka
- Department of Computer Science, Czech Technical University in Prague, Karlovo náměstí 13, 121 35, Prague 2, Czech Republic
| | - Filip Železný
- Department of Computer Science, Czech Technical University in Prague, Karlovo náměstí 13, 121 35, Prague 2, Czech Republic
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Henriques R, Madeira SC. BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge. Algorithms Mol Biol 2016; 11:23. [PMID: 27651825 PMCID: PMC5024481 DOI: 10.1186/s13015-016-0085-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/16/2016] [Indexed: 11/10/2022] Open
Abstract
Background Biclustering has been largely used in biological data analysis, enabling the discovery of putative functional modules from omic and network data. Despite the recognized importance of incorporating domain knowledge to guide biclustering and guarantee a focus on relevant and non-trivial biclusters, this possibility has not yet been comprehensively addressed. This results from the fact that the majority of existing algorithms are only able to deliver sub-optimal solutions with restrictive assumptions on the structure, coherency and quality of biclustering solutions, thus preventing the up-front satisfaction of knowledge-driven constraints. Interestingly, in recent years, a clearer understanding of the synergies between pattern mining and biclustering gave rise to a new class of algorithms, termed as pattern-based biclustering algorithms. These algorithms, able to efficiently discover flexible biclustering solutions with optimality guarantees, are thus positioned as good candidates for knowledge incorporation. In this context, this work aims to bridge the current lack of solid views on the use of background knowledge to guide (pattern-based) biclustering tasks. Methods This work extends (pattern-based) biclustering algorithms to guarantee the satisfiability of constraints derived from background knowledge and to effectively explore efficiency gains from their incorporation. In this context, we first show the relevance of constraints with succinct, (anti-)monotone and convertible properties for the analysis of expression data and biological networks. We further show how pattern-based biclustering algorithms can be adapted to effectively prune of the search space in the presence of such constraints, as well as be guided in the presence of biological annotations. Relying on these contributions, we propose BiClustering with Constraints using PAttern Mining (BiC2PAM), an extension of BicPAM and BicNET biclustering algorithms. Results Experimental results on biological data demonstrate the importance of incorporating knowledge within biclustering to foster efficiency and enable the discovery of non-trivial biclusters with heightened biological relevance. Conclusions This work provides the first comprehensive view and sound algorithm for biclustering biological data with constraints derived from user expectations, knowledge repositories and/or literature.
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Henriques R, Madeira SC. Pattern-Based Biclustering with Constraints for Gene Expression Data Analysis. PROGRESS IN ARTIFICIAL INTELLIGENCE 2015. [DOI: 10.1007/978-3-319-23485-4_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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