1
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Jia W, Ma X. Clustering of multi-layer networks with structural relations and conservation of features. Appl Soft Comput 2023. [DOI: 10.1016/j.asoc.2023.110272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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2
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A Multiagent Memetic Optimization Algorithm Based on Temporal Asymptotic Surprise in Complex Networks to Reveal the Structure of the Dynamic Community. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:6976875. [PMID: 35814542 PMCID: PMC9262479 DOI: 10.1155/2022/6976875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/08/2022] [Accepted: 06/01/2022] [Indexed: 02/02/2023]
Abstract
Complex networks are used in a variety of applications. Revealing the structure of a community is one of the essential features of a network, during which remote communities are discovered in a complex network. In the real world, dynamic networks are evolving, and the problem of tracking and detecting communities at different time intervals is raised. We can use dynamic graphs to model these types of networks. This paper proposes a multiagent optimization memetic algorithm in complex networks to detect dynamic communities and calls it DYNMAMA (dynamic multiagent memetic algorithm). The temporal asymptotic surprise is used as an evaluation function of the algorithm. In the proposed algorithm, work is done on dynamic data. This algorithm does not need to specify the number of communities in advance and meets the time smoothing limit, and this applies to dynamic real-world and synthetic networks. The results of the performance of the evaluation function show that this proposed algorithm can find an optimal and more convergent solution compared to modern approaches.
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3
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Joint multi-label learning and feature extraction for temporal link prediction. PATTERN RECOGNITION 2022. [DOI: 10.1016/j.patcog.2021.108216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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4
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Shi K, Lin W, Zhao XM. Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2514-2525. [PMID: 32305934 DOI: 10.1109/tcbb.2020.2986387] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular biomarkers are certain molecules or set of molecules that can be of help for diagnosis or prognosis of diseases or disorders. In the past decades, thanks to the advances in high-throughput technologies, a huge amount of molecular 'omics' data, e.g., transcriptomics and proteomics, have been accumulated. The availability of these omics data makes it possible to screen biomarkers for diseases or disorders. Accordingly, a number of computational approaches have been developed to identify biomarkers by exploring the omics data. In this review, we present a comprehensive survey on the recent progress of identification of molecular biomarkers with machine learning approaches. Specifically, we categorize the machine learning approaches into supervised, un-supervised and recommendation approaches, where the biomarkers including single genes, gene sets and small gene networks. In addition, we further discuss potential problems underlying bio-medical data that may pose challenges for machine learning, and provide possible directions for future biomarker identification.
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Strub MD, Gao L, Tan K, McCray PB. Analysis of multiple gene co-expression networks to discover interactions favoring CFTR biogenesis and ΔF508-CFTR rescue. BMC Med Genomics 2021; 14:258. [PMID: 34717611 PMCID: PMC8557508 DOI: 10.1186/s12920-021-01106-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/20/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND We previously reported that expression of a miR-138 mimic or knockdown of SIN3A in primary cultures of cystic fibrosis (CF) airway epithelia increased ΔF508-CFTR mRNA and protein levels, and partially restored CFTR-dependent chloride transport. Global mRNA transcript profiling in ΔF508-CFBE cells treated with miR-138 mimic or SIN3A siRNA identified two genes, SYVN1 and NEDD8, whose inhibition significantly increased ΔF508-CFTR trafficking, maturation, and function. Little is known regarding the dynamic changes in the CFTR gene network during such rescue events. We hypothesized that analysis of condition-specific gene networks from transcriptomic data characterizing ΔF508-CFTR rescue could help identify dynamic gene modules associated with CFTR biogenesis. METHODS We applied a computational method, termed M-module, to analyze multiple gene networks, each of which exhibited differential activity compared to a baseline condition. In doing so, we identified both unique and shared gene pathways across multiple differential networks. To construct differential networks, gene expression data from CFBE cells were divided into three groups: (1) siRNA inhibition of NEDD8 and SYVN1; (2) miR-138 mimic and SIN3A siRNA; and (3) temperature (27 °C for 24 h, 40 °C for 24 h, and 27 °C for 24 h followed by 40 °C for 24 h). RESULTS Interrogation of individual networks (e.g., NEDD8/SYVN1 network), combinations of two networks (e.g., NEDD8/SYVN1 + temperature networks), and all three networks yielded sets of 1-modules, 2-modules, and 3-modules, respectively. Gene ontology analysis revealed significant enrichment of dynamic modules in pathways including translation, protein metabolic/catabolic processes, protein complex assembly, and endocytosis. Candidate CFTR effectors identified in the analysis included CHURC1, GZF1, and RPL15, and siRNA-mediated knockdown of these genes partially restored CFTR-dependent transepithelial chloride current to ΔF508-CFBE cells. CONCLUSIONS The ability of the M-module to identify dynamic modules involved in ΔF508 rescue provides a novel approach for studying CFTR biogenesis and identifying candidate suppressors of ΔF508.
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Affiliation(s)
- Matthew D Strub
- Department of Pediatrics, University of Iowa, 6320 PBDB, 169 Newton Road, Iowa City, IA, 52242, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52245, USA
| | - Long Gao
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Tan
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul B McCray
- Department of Pediatrics, University of Iowa, 6320 PBDB, 169 Newton Road, Iowa City, IA, 52242, USA. .,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52245, USA.
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6
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Wang Y, Ma X. Joint nonnegative matrix factorization and network embedding for graph co-clustering. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2021.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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7
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Dou Z, Ma X. Inferring Functional Epigenetic Modules by Integrative Analysis of Multiple Heterogeneous Networks. Front Genet 2021; 12:706952. [PMID: 34504516 PMCID: PMC8421682 DOI: 10.3389/fgene.2021.706952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/29/2021] [Indexed: 02/02/2023] Open
Abstract
Gene expression and methylation are critical biological processes for cells, and how to integrate these heterogeneous data has been extensively investigated, which is the foundation for revealing the underlying patterns of cancers. The vast majority of the current algorithms fuse gene methylation and expression into a network, failing to fully explore the relations and heterogeneity of them. To resolve these problems, in this study we define the epigenetic modules as a gene set whose members are co-methylated and co-expressed. To address the heterogeneity of data, we construct gene co-expression and co-methylation networks, respectively. In this case, the epigenetic module is characterized as a common module in multiple networks. Then, a non-negative matrix factorization-based algorithm that jointly clusters the co-expression and co-methylation networks is proposed for discovering the epigenetic modules (called Ep-jNMF). Ep-jNMF is more accurate than the baselines on the artificial data. Moreover, Ep-jNMF identifies more biologically meaningful modules. And the modules can predict the subtypes of cancers. These results indicate that Ep-jNMF is efficient for the integration of expression and methylation data.
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Affiliation(s)
- Zengfa Dou
- The 20-th Research Institute, China Electronics Technology Group Corporation, Xi'an, China
| | - Xiaoke Ma
- School of Computer Science and Technology, Xidian University, Xi'an, China
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8
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Wang Y, Xia Z, Deng J, Xie X, Gong M, Ma X. TLGP: a flexible transfer learning algorithm for gene prioritization based on heterogeneous source domain. BMC Bioinformatics 2021; 22:274. [PMID: 34433414 PMCID: PMC8386056 DOI: 10.1186/s12859-021-04190-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/12/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Gene prioritization (gene ranking) aims to obtain the centrality of genes, which is critical for cancer diagnosis and therapy since keys genes correspond to the biomarkers or targets of drugs. Great efforts have been devoted to the gene ranking problem by exploring the similarity between candidate and known disease-causing genes. However, when the number of disease-causing genes is limited, they are not applicable largely due to the low accuracy. Actually, the number of disease-causing genes for cancers, particularly for these rare cancers, are really limited. Therefore, there is a critical needed to design effective and efficient algorithms for gene ranking with limited prior disease-causing genes. RESULTS In this study, we propose a transfer learning based algorithm for gene prioritization (called TLGP) in the cancer (target domain) without disease-causing genes by transferring knowledge from other cancers (source domain). The underlying assumption is that knowledge shared by similar cancers improves the accuracy of gene prioritization. Specifically, TLGP first quantifies the similarity between the target and source domain by calculating the affinity matrix for genes. Then, TLGP automatically learns a fusion network for the target cancer by fusing affinity matrix, pathogenic genes and genomic data of source cancers. Finally, genes in the target cancer are prioritized. The experimental results indicate that the learnt fusion network is more reliable than gene co-expression network, implying that transferring knowledge from other cancers improves the accuracy of network construction. Moreover, TLGP outperforms state-of-the-art approaches in terms of accuracy, improving at least 5%. CONCLUSION The proposed model and method provide an effective and efficient strategy for gene ranking by integrating genomic data from various cancers.
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Affiliation(s)
- Yan Wang
- School of Computer Science and Technology, Xidian University, South TaiBai Road, Xi’an, China
- Department of Library, Xidian University, South TaiBai Road, Xi’an, China
| | - Zuheng Xia
- School of Computer Science and Technology, Xidian University, South TaiBai Road, Xi’an, China
| | - Jingjing Deng
- Department of Computer Science, Swansea University, Bay, UK
| | - Xianghua Xie
- Department of Computer Science, Swansea University, Bay, UK
| | - Maoguo Gong
- School of Electronic Engineering, Xidian University, South TaiBai Road, Xi’an, China
| | - Xiaoke Ma
- School of Computer Science and Technology, Xidian University, South TaiBai Road, Xi’an, China
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9
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Li D, Zhong X, Dou Z, Gong M, Ma X. Detecting dynamic community by fusing network embedding and nonnegative matrix factorization. Knowl Based Syst 2021. [DOI: 10.1016/j.knosys.2021.106961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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10
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Li D, Zhang S, Ma X. Dynamic Module Detection in Temporal Attributed Networks of cancers. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 19:2219-2230. [PMID: 33780342 DOI: 10.1109/tcbb.2021.3069441] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Tracking the dynamic modules during cancer progression is essential for studying cancer pathogenesis, diagnosis and therapy. However, current algorithms only focus on detecting dynamic modules from temporal cancer networks without integrating the heterogeneous genomic data, thereby resulting in undesirable performance. To attack this issue, a novel algorithm (aka TANMF) is proposed to detect dynamic modules in cancer temporal attributed networks, which integrates the temporal networks and gene attributes. To obtain the dynamic modules, the temporality and gene attributed are incorporated into an overall objective function, which transforms the dynamic module detection into an optimization problem. TANMF jointly decomposes the snapshots at two subsequent time steps to obtain the latent features of dynamic modules, where the attributes are fused via regulations. Furthermore, L1 constraint is imposed to improve the robustness. Experimental results demonstrate that TANMF is more accurate than state-of-the-art methods in terms of accuracy. By applying TANMF to breast cancer data, the obtained dynamic modules are more enriched by the known pathways and associated with the survival time of patients. The proposed model and algorithm provide an effective way for the integrative analysis of heterogeneous omics.
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11
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Savino A, Provero P, Poli V. Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. Int J Mol Sci 2020; 21:E9461. [PMID: 33322692 PMCID: PMC7764314 DOI: 10.3390/ijms21249461] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 02/02/2023] Open
Abstract
Biological systems respond to perturbations through the rewiring of molecular interactions, organised in gene regulatory networks (GRNs). Among these, the increasingly high availability of transcriptomic data makes gene co-expression networks the most exploited ones. Differential co-expression networks are useful tools to identify changes in response to an external perturbation, such as mutations predisposing to cancer development, and leading to changes in the activity of gene expression regulators or signalling. They can help explain the robustness of cancer cells to perturbations and identify promising candidates for targeted therapy, moreover providing higher specificity with respect to standard co-expression methods. Here, we comprehensively review the literature about the methods developed to assess differential co-expression and their applications to cancer biology. Via the comparison of normal and diseased conditions and of different tumour stages, studies based on these methods led to the definition of pathways involved in gene network reorganisation upon oncogenes' mutations and tumour progression, often converging on immune system signalling. A relevant implementation still lagging behind is the integration of different data types, which would greatly improve network interpretability. Most importantly, performance and predictivity evaluation of the large variety of mathematical models proposed would urgently require experimental validations and systematic comparisons. We believe that future work on differential gene co-expression networks, complemented with additional omics data and experimentally tested, will considerably improve our insights into the biology of tumours.
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Affiliation(s)
- Aurora Savino
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy
| | - Paolo Provero
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, Corso Massimo D’Ázeglio 52, 10126 Turin, Italy;
- Center for Omics Sciences, Ospedale San Raffaele IRCCS, Via Olgettina 60, 20132 Milan, Italy
| | - Valeria Poli
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy
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12
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Co-regularized nonnegative matrix factorization for evolving community detection in dynamic networks. Inf Sci (N Y) 2020. [DOI: 10.1016/j.ins.2020.04.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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13
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Ma X, Sun P, Gong M. An integrative framework of heterogeneous genomic data for cancer dynamic modules based on matrix decomposition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 19:305-316. [PMID: 32750874 DOI: 10.1109/tcbb.2020.3004808] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cancer progression is dynamic, and tracking dynamic modules is promising for cancer diagnosis and therapy. Accumulated genomic data provide us an opportunity to investigate the underlying mechanisms of cancers. However, as far as we know, no algorithm has been designed for dynamic modules by integrating heterogeneous omics data. To address this issue, we propose an integrative framework for dynamic module detection based on regularized nonnegative matrix factorization method (DrNMF) by integrating the gene expression and protein interaction network. To remove the heterogeneity of genomic data, we divide the samples of expression profiles into groups to construct gene co-expression networks. To characterize the dynamics of modules, the temporal smoothness framework is adopted, in which the gene co-expression network at the previous stage and protein interaction network are incorporated into the objective function of DrNMF via regularization. The experimental results demonstrate that DrNMF is superior to state-of-the-art methods in terms of accuracy. For breast cancer data, the obtained dynamic modules are more enriched by the known pathways, and can be used to predict the stages of cancers and survival time of patients. The proposed model and algorithm provide an effective integrative analysis of heterogeneous genomic data for cancer progression.
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14
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Huang Z, Zhong X, Wang Q, Gong M, Ma X. Detecting community in attributed networks by dynamically exploring node attributes and topological structure. Knowl Based Syst 2020. [DOI: 10.1016/j.knosys.2020.105760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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15
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16
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Di Nanni N, Bersanelli M, Milanesi L, Mosca E. Network Diffusion Promotes the Integrative Analysis of Multiple Omics. Front Genet 2020; 11:106. [PMID: 32180795 PMCID: PMC7057719 DOI: 10.3389/fgene.2020.00106] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/29/2020] [Indexed: 02/01/2023] Open
Abstract
The development of integrative methods is one of the main challenges in bioinformatics. Network-based methods for the analysis of multiple gene-centered datasets take into account known and/or inferred relations between genes. In the last decades, the mathematical machinery of network diffusion—also referred to as network propagation—has been exploited in several network-based pipelines, thanks to its ability of amplifying association between genes that lie in network proximity. Indeed, network diffusion provides a quantitative estimation of network proximity between genes associated with one or more different data types, from simple binary vectors to real vectors. Therefore, this powerful data transformation method has also been increasingly used in integrative analyses of multiple collections of biological scores and/or one or more interaction networks. We present an overview of the state of the art of bioinformatics pipelines that use network diffusion processes for the integrative analysis of omics data. We discuss the fundamental ways in which network diffusion is exploited, open issues and potential developments in the field. Current trends suggest that network diffusion is a tool of broad utility in omics data analysis. It is reasonable to think that it will continue to be used and further refined as new data types arise (e.g. single cell datasets) and the identification of system-level patterns will be considered more and more important in omics data analysis.
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Affiliation(s)
- Noemi Di Nanni
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.,Department of Industrial and Information Engineering, University of Pavia, Pavia, Italy
| | - Matteo Bersanelli
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,National Institute of Nuclear Physics (INFN), Bologna, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
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17
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Detecting evolving communities in dynamic networks using graph regularized evolutionary nonnegative matrix factorization. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 2019. [DOI: 10.1016/j.physa.2019.121279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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18
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Li G, Liu KY, Qiu ZP. An integrative module analysis of DNA methylation landscape in aging. Exp Ther Med 2019; 17:3411-3416. [PMID: 30988719 PMCID: PMC6447821 DOI: 10.3892/etm.2019.7334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 02/06/2019] [Indexed: 02/02/2023] Open
Abstract
To investigate the molecular mechanism of aging, the combination of module analysis and DNA methylation data was used to detect dynamically controlled modules for aging. Multiple differential expression networks (DENs) were constructed based on the microarray profiles across different aging groups (<70 years, 70–80 years, and >80 years). Next, a module-based approach was utilized to extract the common candidate modules across all age groups. We used Module Connectivity Dynamic Score (MCDS) to quantify the connectivity change of the common modules among the different age groups. Functional analyses were implemented for the genes in the common modules to further identify the significant biological processes. A total of two DENs were constructed. Overall 657 informative genes were screened out. When false discovery rate (FDR) was set as 0.05, we found that 148 modules were significant. Only 1 significant 2-differential modules (DMs) (module 493) with dynamic changes was discovered. Significantly, the genes in the module 493 participated in 7 significant pathways, including pentose phosphate pathway, carbon metabolism, and citrate cycle (TCA cycle). In conclusion, pathway functions [pentose phosphate pathway, carbon metabolism, citrate cycle (TCA cycle), chromosomal instability, ateroid biosynthesis, PPAR signaling pathway, and immune response] may serve as potential therapeutic targets in aging.
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Affiliation(s)
- Gang Li
- Department of Orthopedics, School of Medicine, Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Ke-Yu Liu
- Department of Orthopedics, School of Medicine, Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Zhong-Peng Qiu
- Department of Orthopedics, School of Medicine, Shihezi University, Shihezi, Xinjiang 832000, P.R. China
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Ma X, Dong D, Wang Q. Community Detection in Multi-Layer Networks Using Joint Nonnegative Matrix Factorization. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2019. [DOI: 10.1109/tkde.2018.2832205] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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20
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Ma X, Sun P, Zhang ZY. An Integrative Framework for Protein Interaction Network and Methylation Data to Discover Epigenetic Modules. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:1855-1866. [PMID: 29994031 DOI: 10.1109/tcbb.2018.2831666] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
DNA methylation is a critical epigenetic modification that plays an important role in cancers. The available algorithms fail to fully characterize epigenetic modules. To address this issue, we first characterize the epigenetic module as a group of well-connected genes in the protein interaction network and are also co-methylated based on gene methylation profiles. Then, the epigenetic module discovery problem is transformed into an optimization problem. Then, a regularized nonnegative matrix factorization algorithm for methylation modules (RNMF-MM) is presented, where the co-methylation constraint is treated as a regularizer. Using the artificial networks with known module structure, we demonstrate that the proposed algorithm outperforms state-of-the-art approaches in terms of accuracy. On the basis of breast cancer methylation data and protein interaction network, the RNMF-MM algorithm discovers methylation modules that are significantly more enriched by the known pathways than those obtained by other algorithms. These modules serve as biomarkers for predicting cancer stages and estimating survival time of patients. The proposed model and algorithm provide an effective way for the integrative analysis of protein interaction network and methylation data.
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21
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Zhang E, Ma X. Regularized Multi-View Subspace Clustering for Common Modules Across Cancer Stages. Molecules 2018; 23:molecules23051016. [PMID: 29701681 PMCID: PMC6102576 DOI: 10.3390/molecules23051016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 02/01/2023] Open
Abstract
Discovering the common modules that are co-expressed across various stages can lead to an improved understanding of the underlying molecular mechanisms of cancers. There is a shortage of efficient tools for integrative analysis of gene expression and protein interaction networks for discovering common modules associated with cancer progression. To address this issue, we propose a novel regularized multi-view subspace clustering (rMV-spc) algorithm to obtain a representation matrix for each stage and a joint representation matrix that balances the agreement across various stages. To avoid the heterogeneity of data, the protein interaction network is incorporated into the objective of rMV-spc via regularization. Based on the interior point algorithm, we solve the optimization problem to obtain the common modules. By using artificial networks, we demonstrate that the proposed algorithm outperforms state-of-the-art methods in terms of accuracy. Furthermore, the rMV-spc discovers common modules in breast cancer networks based on the breast data, and these modules serve as biomarkers to predict stages of breast cancer. The proposed model and algorithm effectively integrate heterogeneous data for dynamic modules.
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Affiliation(s)
- Enli Zhang
- School of Computer Science and Technology, Xidian University, Xi'an 710071, Shaanxi, China.
| | - Xiaoke Ma
- School of Computer Science and Technology, Xidian University, Xi'an 710071, Shaanxi, China.
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22
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Zhang W, Wang SL. An efficient strategy for identifying cancer-related key genes based on graph entropy. Comput Biol Chem 2018; 74:142-148. [PMID: 29609142 DOI: 10.1016/j.compbiolchem.2018.03.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/22/2018] [Accepted: 03/20/2018] [Indexed: 02/02/2023]
Abstract
Gene networks are beneficial to identify functional genes that are highly relevant to clinical outcomes. Most of the current methods require information about the interaction of genes or proteins to construct genetic network connection. However, the conclusion of these methods may be bias because of the current incompleteness of human interactome. In this paper, we propose an efficient strategy to use gene expression data and gene mutation data for identifying cancer-related key genes based on graph entropy (iKGGE). Firstly, we construct a gene network using only gene expression data based on the sparse inverse covariance matrix, then, cluster genes use the algorithm of parallel maximal cliques for quickly obtaining a series of subgraphs, and at last, we introduce a novel metric that combine graph entropy and the influence of upstream gene mutations information to measure the impact factors of genes. Testing of the three available cancer datasets shows that our strategy can effectively extract key genes that may play distinct roles in tumorigenesis, and the cancer patient risk groups are well predicted based on key genes.
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Affiliation(s)
- Wei Zhang
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, Hunan, 410082, China.
| | - Shu-Lin Wang
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, Hunan, 410082, China.
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23
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Ma X, Sun P, Wang Y. Graph regularized nonnegative matrix factorization for temporal link prediction in dynamic networks. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 2018. [DOI: 10.1016/j.physa.2017.12.092] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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24
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Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks. Molecules 2017; 22:molecules22122228. [PMID: 29240706 PMCID: PMC6149918 DOI: 10.3390/molecules22122228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 02/02/2023] Open
Abstract
The advances in biological technologies make it possible to generate data for multiple conditions simultaneously. Discovering the condition-specific modules in multiple networks has great merit in understanding the underlying molecular mechanisms of cells. The available algorithms transform the multiple networks into a single objective optimization problem, which is criticized for its low accuracy. To address this issue, a multi-objective genetic algorithm for condition-specific modules in multiple networks (MOGA-CSM) is developed to discover the condition-specific modules. By using the artificial networks, we demonstrate that the MOGA-CSM outperforms state-of-the-art methods in terms of accuracy. Furthermore, MOGA-CSM discovers stage-specific modules in breast cancer networks based on The Cancer Genome Atlas (TCGA) data, and these modules serve as biomarkers to predict stages of breast cancer. The proposed model and algorithm provide an effective way to analyze multiple networks.
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Silymarin-mediated regulation of the cell cycle and DNA damage response exerts antitumor activity in human hepatocellular carcinoma. Oncol Lett 2017; 15:885-892. [PMID: 29399153 PMCID: PMC5772825 DOI: 10.3892/ol.2017.7425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/26/2017] [Indexed: 02/02/2023] Open
Abstract
A novel module-search algorithm method was used to screen for potential signatures and investigate the molecular mechanisms of inhibiting hepatocellular carcinoma (HCC) growth following treatment with silymarin (SM). The modules algorithm was used to identify the modules via three major steps: i) Seed gene selection; ii) module search by seed expansion and entropy minimization; and iii) module refinement. The statistical significance of modules was computed to select the differential modules (DMs), followed by the identification of core modules using the attract method. Pathway analysis for core modules was implemented to identify the biological functions associated with the disease. Subsequently, results were verified in an independent sample set using reverse transcription polymerase chain reaction (RT-PCR). In total, 18 seed genes and 12 DMs (modules 1-12) were identified. The core modules were isolated using gene expression data. Overall, there were 4 core modules (modules 11, 5, 6 and 12). Additionally, DNA topoisomerase 2-binding protein 1 (TOPBP1), non-structural maintenance of chromosomes condensing I complex subunit H, nucleolar and spindle associated protein 1 (NUSAP1) and cell division cycle associated 3 (CDCA3) were the initial seed genes of module 11, 5, 6 and 12, respectively. Pathway results revealed that cell cycle signaling pathway was enriched by all core modules simultaneously. RT-PCR results indicated that the level of CDCA3, TOPBP1 and NUSAP1 in SM-treated HCC samples was markedly decreased compared with that in non-SM-treated HCC. No statistically significant difference between the transcriptional levels of CDCA3 in SM-treated and non-treated HCC groups was identified, although CDCA3 expression was increased in the treated group compared with the untreated group. Furthermore, although the expression level of TOPBP1 and NUSAP1 in the SM-treated group was decreased compared with that in the normal group, no significant difference was observed. From the results of the present study it can be inferred that TOPBP1, NUSAP1 and CDCA3 of the core modules may serve notable functions in SM-associated growth suppression of HCC.
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Ma X, Sun P, Qin G. Nonnegative matrix factorization algorithms for link prediction in temporal networks using graph communicability. PATTERN RECOGNITION 2017. [DOI: 10.1016/j.patcog.2017.06.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Ma X, Sun P, Qin G. Identifying condition-specific modules by clustering multiple networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 15:1636-1648. [PMID: 29028204 DOI: 10.1109/tcbb.2017.2761339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Condition-specific modules in multiple networks must be determined to reveal the underlying molecular mechanisms of diseases. Current algorithms exhibit limitations such as low accuracy and high sensitivity to the number of networks because these algorithms discover condition-specific modules in multiple networks by separating specificity and modularity of modules. To overcome these limitations, we characterize condition-specific module as a group of genes whose connectivity is strong in the corresponding network and weak in other networks; this strategy can accurately depict the topological structure of condition-specific modules. We then transform the condition-specific module discovery problem into a clustering problem in multiple networks. We develop an efficient heuristic algorithm for the Specific Modules in Multiple Networks (SMMN), which discovers the condition-specific modules by considering multiple networks. By using the artificial networks, we demonstrate that SMMN outperforms state-of-the-art methods. In breast cancer networks, stage-specific modules discovered by SMMN are more discriminative in predicting cancer stages than those obtained by other techniques. In pan-cancer networks, cancer-specific modules are more likely to associate with survival time of patients, which is critical for cancer therapy.
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Wang Z, Yan X, Zhao C. Dynamical differential networks and modules inferring disrupted genes associated with the progression of Alzheimer's disease. Exp Ther Med 2017; 14:2969-2975. [PMID: 28966679 PMCID: PMC5613183 DOI: 10.3892/etm.2017.4905] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 03/06/2017] [Indexed: 02/02/2023] Open
Abstract
In order to understand the pathogenic factors that initiate the processes of Alzheimer's disease (AD), a method of inference of multiple differential modules (iMDM) to conduct analysis was performed on the gene expression profile of AD. A total of 11,089 genes and 588,391 interactions were gained based on the gene expression profile and protein-protein interaction network. Subsequently, three differential co-expression networks (DCNs) were constructed with the same nodes but different interactions, and eight multiple differential modules (M-DMs) were identified. Furthermore, by performing Module Connectivity Dynamic Score to quantify the change in the connectivity of component modules, two M-DMs were identified: Module 1 (P=0.0419) and 2 (P=0.0419; adjusted, P≤0.05). Finally, hub genes of MDH1, NDUFAB1, NDUFB5, DDX1 and MRPS35 were gained via topological analysis conducted on the 2 M-DMs. In conclusion, the method of iMDM was suitable for conducting analysis on AD. By applying iMDM, 2 M-DMs were successfully identified and the MDH1, NDUFAB1, NDUFB5, DDX1 and MRPS35 genes were predicted to be important during the occurrence and development of AD.
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Affiliation(s)
- Zhengling Wang
- Office of Medical Social Work, Yidu Central Hospital of Weifang, Weifang, Shandong 262500, P.R. China
| | - Xinling Yan
- Department of Neurology, Yidu Central Hospital of Weifang, Weifang, Shandong 262500, P.R. China
| | - Chenghua Zhao
- Department of Neurology, Yidu Central Hospital of Weifang, Weifang, Shandong 262500, P.R. China
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Modeling osteosarcoma progression by measuring the connectivity dynamics using an inference of multiple differential modules algorithm. Mol Med Rep 2017; 16:1047-1054. [PMID: 28586048 PMCID: PMC5562023 DOI: 10.3892/mmr.2017.6703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 03/08/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding the dynamic changes in connectivity of molecular pathways is important for determining disease prognosis. Thus, the current study used an inference of multiple differential modules (iMDM) algorithm to identify the connectivity changes of sub-network to predict the progression of osteosarcoma (OS) based on the microarray data of OS at four Huvos grades. Initially, multiple differential co-expression networks (M-DCNs) were constructed, and weight values were assigned for each edge, followed by detection of seed genes in M-DCNs according to the topological properties. Using these seed gene as a start, an iMDM algorithm was utilized to identify the multiple candidate modules. The statistical significance was determined to select multiple differential modules (M-DMs) based on the null score distribution of candidate modules generated using randomized networks. Additionally, the significance of Module Connectivity Dynamic Score (MCDS) to quantify the dynamic change of M-DMs connectivity. Further, DAVID was employed for KEGG pathway enrichment analysis of genes in dynamic modules. In addition to the basal condition, four conditions, OS grade 1–4, were also included (M=4). In total, 4 DCNs were constructed, and each of them included 2,138 edges and 272 nodes. A total of 13 genes were identified and termed ‘seed genes’ based on the z-score distribution of 272 nodes in DCNs. Following the module search, module refinement and statistical significance analysis, a total of four 4-DMs (modules 1, 2, 3 and 4) were identified. Only one significant 4-DM (module 3 in the DCNs of grade 1, 2, 3 and 4 OS) with dynamic changes was detected when the MCDS of real 4-DMs were compared to a null distribution of MCDS of random 4-DMs. Notably, the genes of the dynamic module (module 3) were enriched in two significant pathway terms, ubiquitin-mediated proteolysis and ribosome. The seed genes with the highest degrees included protein phosphatase 1 regulatory subunit 12A (PPP1R12A), UTP3, small subunit processome component homolog (UTP3), prostaglandin E synthase 3 (PTGES3). Thus, pathway functions (ubiquitin-mediated proteolysis and ribosome) and several seed genes (PPP1R12A, UTP3, and PTGES3) in the dynamic module 3 may be associated with the progression of OS and may serve as potential therapeutic targets in OS.
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Zhou J, Chen C, Li HF, Hu YJ, Xie HL. Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks. Mol Med Rep 2017; 16:696-702. [PMID: 28560382 PMCID: PMC5482131 DOI: 10.3892/mmr.2017.6641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 03/02/2017] [Indexed: 02/02/2023] Open
Abstract
The progression of glioblastoma (GBM) is driven by dynamic alterations in the activity and connectivity of gene pathways. Revealing these dynamic events is necessary in order to understand the pathological mechanisms of, and develop effective treatments for, GBM. The present study aimed to investigate dynamic alterations in pathway activity and connectivity across radiotherapy and chemoradiation conditions in GBM, and to give system-level insights into molecular mechanisms for GBM therapy. A total of two differential co-expression networks (DCNs) were constructed using Pearson correlation coefficient analysis and one sided t-tests, based on gene expression profiles and protein-protein interaction networks, one for each condition. Subsequently, shared differential modules across DCNs were detected via significance analysis for candidate modules, which were obtained according to seed selection, module search by seed expansion and refinement of searched modules. As condition-specific differential modules mediate differential biological processes, the module connectivity dynamic score (MCDS) was implemented to explore dynamic alterations among them. Based on DCNs with 287 nodes and 1,052 edges, a total of 28 seed genes and seven candidate modules were identified. Following significance analysis, five shared differential modules were identified in total. Dynamic alterations among these differential modules were identified using the MCDS, and one module with significant dynamic alterations was identified, termed the dynamic module. The present study revealed the dynamic alterations of shared differential modules, identified one dynamic module between the radiotherapy and chemoradiation conditions, and demonstrated that pathway dynamics may applied to the study of the pathogenesis and therapy of GBM.
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Affiliation(s)
- Jia Zhou
- Department of Geratology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Chao Chen
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Hua-Feng Li
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Yu-Jie Hu
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Hong-Ling Xie
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
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Ma X, Yu L, Wang P, Yang X. Discovering DNA methylation patterns for long non-coding RNAs associated with cancer subtypes. Comput Biol Chem 2017; 69:164-170. [PMID: 28501295 DOI: 10.1016/j.compbiolchem.2017.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 02/01/2023]
Abstract
Despite growing evidence demonstrates that the long non-coding ribonucleic acids (lncRNAs) are critical modulators for cancers, the knowledge about the DNA methylation patterns of lncRNAs is quite limited. We develop a systematic analysis pipeline to discover DNA methylation patterns for lncRNAs across multiple cancer subtypes from probe, gene and network levels. By using The Cancer Genome Atlas (TCGA) breast cancer methylation data, the pipeline discovers various DNA methylation patterns for lncRNAs across four major subtypes such as luminal A, luminal B, her2-enriched as well as basal-like. On the probe and gene level, we find that both differentially methylated probes and lncRNAs are subtype specific, while the lncRNAs are not as specific as probes. On the network level, the pipeline constructs differential co-methylation lncRNA network for each subtype. Then, it identifies both subtype specific and common lncRNA modules by simultaneously analyzing multiple networks. We show that the lncRNAs in subtype specific and common modules differ greatly in terms of topological structure, sequence conservation as well as expression. Furthermore, the subtype specific lncRNA modules serve as biomarkers to improve significantly the accuracy of breast cancer subtypes prediction. Finally, the common lncRNA modules associate with survival time of patients, which is critical for cancer therapy.
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Affiliation(s)
- Xiaoke Ma
- School of Computer Science and Technology, Xidian University, No.2 South Taibai Road, Xi'an, Shaanxi, China; Xidian-Ningbo Information Technology Institute, Xidian University, No. 777 Zhongguanxi Road, Ningbo City, China.
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, No.2 South Taibai Road, Xi'an, Shaanxi, China
| | - Peizhuo Wang
- School of Computer Science and Technology, Xidian University, No.2 South Taibai Road, Xi'an, Shaanxi, China
| | - Xiaofei Yang
- School of Computer Science and Technology, Xidian University, No.2 South Taibai Road, Xi'an, Shaanxi, China
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Ma X, Dong D. Evolutionary Nonnegative Matrix Factorization Algorithms for Community Detection in Dynamic Networks. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2017. [DOI: 10.1109/tkde.2017.2657752] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Han L, Chen C, Liu CH, Zhang M, Liang L. Revealing differential modules in uveal melanoma by analyzing differential networks. Mol Med Rep 2017; 15:2261-2266. [PMID: 28260033 DOI: 10.3892/mmr.2017.6232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 12/28/2016] [Indexed: 02/02/2023] Open
Abstract
The aim of the present study was to investigate differential modules (DMs) between uveal melanoma (UM) and normal conditions by examining differential networks. Based on a gene expression profile collected from the ArrayExpress database, the inference of DMs involved three steps: The first step was construction of a differential co‑expression network (DCN); second, the module algorithm was adapted to identify the DMs presented in DCN; finally, the statistical significance of DMs were assessed based on the null score distribution of DMs generated using randomized networks. A DCN with 309 nodes and 3,729 edges was obtained, and 30 seed genes from the DCN were examined. Subsequently, one DM, which had 179 nodes and 3,068 edges, was investigated. By utilizing randomized networks, the P‑value for DM was 0.034, therefore, the DM was statically significant between UM and baseline conditions. In conclusion, the present study successfully identified one DM in UM based on DCN and module algorithm, and this DM may be beneficial in revealing the pathological mechanism of UM and provide insight for future investigation of UM.
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Affiliation(s)
- Li Han
- Department of Ophthalmology, Yidu Central Hospital of Weifang, Qingzhou, Shandong 262500, P.R. China
| | - Cui Chen
- Department of Ophthalmology, Yidu Central Hospital of Weifang, Qingzhou, Shandong 262500, P.R. China
| | - Chang-Hui Liu
- Department of Ophthalmology, Dezhou People's Hospital, Dezhou, Shandong 253000, P.R. China
| | - Min Zhang
- Department of Ophthalmology, Jinan Maternity and Child Care Hospital, Jinan, Shandong 250001, P.R. China
| | - Ling Liang
- Department of Ophthalmology, Dezhou People's Hospital, Dezhou, Shandong 253000, P.R. China
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Ma X, Liu Z, Zhang Z, Huang X, Tang W. Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. BMC Bioinformatics 2017; 18:72. [PMID: 28137264 PMCID: PMC5282853 DOI: 10.1186/s12859-017-1490-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/20/2017] [Indexed: 02/05/2023] Open
Abstract
Background With the increase in the amount of DNA methylation and gene expression data, the epigenetic mechanisms of cancers can be extensively investigate. Available methods integrate the DNA methylation and gene expression data into a network by specifying the anti-correlation between them. However, the correlation between methylation and expression is usually unknown and difficult to determine. Results To address this issue, we present a novel multiple network framework for epigenetic modules, namely, Epigenetic Module based on Differential Networks (EMDN) algorithm, by simultaneously analyzing DNA methylation and gene expression data. The EMDN algorithm prevents the specification of the correlation between methylation and expression. The accuracy of EMDN algorithm is more efficient than that of modern approaches. On the basis of The Cancer Genome Atlas (TCGA) breast cancer data, we observe that the EMDN algorithm can recognize positively and negatively correlated modules and these modules are significantly more enriched in the known pathways than those obtained by other algorithms. These modules can serve as bio-markers to predict breast cancer subtypes by using methylation profiles, where positively and negatively correlated modules are of equal importance in the classification of cancer subtypes. Epigenetic modules also estimate the survival time of patients, and this factor is critical for cancer therapy. Conclusions The proposed model and algorithm provide an effective method for the integrative analysis of DNA methylation and gene expression. The algorithm is freely available as an R-package at https://github.com/william0701/EMDN. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1490-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoke Ma
- School of Computer Science and Technology, Xidian University, No.2 South TaiBai Road, Xi'an, People's Republic of China.,Xidian-Ningbo Information Technology Institute, Xidian University, No. 777 Zhongguanxi Road, Ningbo, People's Republic of China
| | - Zaiyi Liu
- Department of Radiology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Zhongshan Road, Guangzhou, People's Republic of China
| | - Zhongyuan Zhang
- School of Statistics and Mathematics, Central University of Finance and Economics, 39 South College Road, Haidian District, Beijing, People's Republic of China
| | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, No.2 South TaiBai Road, Xi'an, People's Republic of China
| | - Wanxin Tang
- Department of Nephrology, West China Hospital, Sichuan University, Wuhou District, Chengdu, People's Republic of China.
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Wang P, Gao L, Ma X. Dynamic community detection based on network structural perturbation and topological similarity. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2017. [DOI: 10.1088/1742-5468/2017/1/013401] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Ma X, Tang W, Wang P, Guo X, Gao L. Extracting Stage-Specific and Dynamic Modules Through Analyzing Multiple Networks Associated with Cancer Progression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 15:647-658. [PMID: 27845671 DOI: 10.1109/tcbb.2016.2625791] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Determining the dynamics of pathways associated with cancer progression is critical for understanding the etiology of diseases. Advances in biological technology have facilitated the simultaneous genomic profiling of multiple patients at different clinical stages, thus generating the dynamic genomic data for cancers. Such data provide enable investigation of the dynamics of related pathways. However, methods for integrative analysis of dynamic genomic data are inadequate. In this study, we develop a novel nonnegative matrix factorization algorithm for dynamic modules ( NMF-DM), which simultaneously analyzes multiple networks for the identification of stage-specific and dynamic modules. NMF-DM applies the temporal smoothness framework by balancing the networks at the current stage and the previous stage. Experimental results indicate that the NMF-DM algorithm is more accurate than the state-of-the-art methods in artificial dynamic networks. In breast cancer networks, NMF-DM reveals the dynamic modules that are important for cancer stage transitions. Furthermore, the stage-specific and dynamic modules have distinct topological and biochemical properties. Finally, we demonstrate that the stage-specific modules significantly improve the accuracy of cancer stage prediction. The proposed algorithm provides an effective way to explore the time-dependent cancer genomic data.
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Anesthetic Propofol-Induced Gene Expression Changes in Patients Undergoing Coronary Artery Bypass Graft Surgery Based on Dynamical Differential Coexpression Network Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2016; 2016:7097612. [PMID: 27437027 PMCID: PMC4942588 DOI: 10.1155/2016/7097612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/12/2016] [Accepted: 06/15/2016] [Indexed: 02/02/2023]
Abstract
We aimed to determine the influence of anesthetic propofol on gene expression in patients treated by coronary artery bypass graft (CABG) surgery based on differential coexpression network (DCN) and to further reveal the novel mechanisms of the cardioprotective effects of propofol. Firstly, we constructed the DCN for disease condition based on Pearson correlation coefficient (PCC) and weight value. Secondly, the inference of modules was applied to search modules from DCN with same members but varied connectivity. Furthermore, we measured the statistical significance of the modules for selecting differential modules (DMs). Finally, attract method was used for DMs analysis to select key modules. Based on the δ value, 11928 edges and 2956 nodes were chosen to construct DCNs. A total of 29 seed genes were selected. Moreover, by quantifying connectivity changes in shared gene modules across different conditions, 8 DMs with higher connectivity dynamics were identified. Then, we extracted key modules using attract method, there were 8 key modules, and the top 3 modules were module 1, 2, and 3. Furthermore, GCG, PPY, and PON1 were initial seed genes of these 3 key modules, respectively. Accordingly, GCG and PON1 might exert important roles in the cardioprotective effects of propofol during CABG.
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Chen C, Ma FW, Du CY, Wang P. Multiple Differential Networks Strategy Reveals Carboplatin and Melphalan-Induced Dynamic Module Changes in Retinoblastoma. Med Sci Monit 2016; 22:1508-15. [PMID: 27144687 PMCID: PMC4917320 DOI: 10.12659/msm.897877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Background Retinoblastoma (RB) is the most common malignant tumor of the eye in childhood. The objective of this paper was to investigate carboplatin (CAR)- and melphalan (MEL)-induced dynamic module changes in RB based on multiple (M) differential networks, and to generate systems-level insights into RB progression. Material/Methods To achieve this goal, we constructed M-differential co-expression networks (DCNs), assigned a weight to each edge, and identified seed genes in M DCNs by ranking genes based on their topological features. Starting with seed genes, a module search was performed to explore candidate modules in CAR and MEL condition. M-DMs were detected according to significance evaluations of M-modules, which originated from refinement of candidate modules. Further, we revealed dynamic changes in M-DM activity and connectivity on the basis of significance of Module Connectivity Dynamic Score (MCDS). Results In the present study, M=2, a total of 21 seed genes were obtained. By assessing module search, refinement, and evaluation, we gained 18 2-DMs. Moreover, 3 significant 2-DMs (Module 1, Module 2, and Module 3) with dynamic changes across CAR and MEL condition were determined, and we denoted them as dynamic modules. Module 1 had 27 nodes of which 6 were seed genes and 56 edges. Module 2 was composed of 28 nodes and 54 edges. A total of 28 nodes interacted with 45 edges presented in Module 3. Conclusions We have identified 3 dynamic modules with changes induced by CAR and MEL in RB, which might give insights in revealing molecular mechanism for RB therapy.
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Affiliation(s)
- Cui Chen
- Department of Ophthalmology, Yidu Central Hospital of Weifang, Qingzhou, Shandong, China (mainland)
| | - Feng-Wei Ma
- Department of Ophthalmology, Yidu Central Hospital of Weifang, Qingzhou, Shandong, China (mainland)
| | - Cui-Yun Du
- Department of Ophthalmology, Yidu Central Hospital of Weifang, Qingzhou, Shandong, China (mainland)
| | - Ping Wang
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China (mainland)
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Ma X, Gao L, Karamanlidis G, Gao P, Lee CF, Garcia-Menendez L, Tian R, Tan K. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PLoS Comput Biol 2015; 11:e1004332. [PMID: 26083688 PMCID: PMC4471235 DOI: 10.1371/journal.pcbi.1004332] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/12/2015] [Indexed: 02/02/2023] Open
Abstract
Development of heart diseases is driven by dynamic changes in both the activity and connectivity of gene pathways. Understanding these dynamic events is critical for understanding pathogenic mechanisms and development of effective treatment. Currently, there is a lack of computational methods that enable analysis of multiple gene networks, each of which exhibits differential activity compared to the network of the baseline/healthy condition. We describe the iMDM algorithm to identify both unique and shared gene modules across multiple differential co-expression networks, termed M-DMs (multiple differential modules). We applied iMDM to a time-course RNA-Seq dataset generated using a murine heart failure model generated on two genotypes. We showed that iMDM achieves higher accuracy in inferring gene modules compared to using single or multiple co-expression networks. We found that condition-specific M-DMs exhibit differential activities, mediate different biological processes, and are enriched for genes with known cardiovascular phenotypes. By analyzing M-DMs that are present in multiple conditions, we revealed dynamic changes in pathway activity and connectivity across heart failure conditions. We further showed that module dynamics were correlated with the dynamics of disease phenotypes during the development of heart failure. Thus, pathway dynamics is a powerful measure for understanding pathogenesis. iMDM provides a principled way to dissect the dynamics of gene pathways and its relationship to the dynamics of disease phenotype. With the exponential growth of omics data, our method can aid in generating systems-level insights into disease progression.
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Affiliation(s)
- Xiaoke Ma
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Long Gao
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
| | - Georgios Karamanlidis
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Peng Gao
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Chi Fung Lee
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lorena Garcia-Menendez
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Rong Tian
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kai Tan
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Dimitrakopoulou K, Vrahatis AG, Bezerianos A. Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism. BMC Genomics 2015; 16:147. [PMID: 25887273 PMCID: PMC4367845 DOI: 10.1186/s12864-015-1256-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/19/2015] [Indexed: 02/02/2023] Open
Abstract
Background The avalanche of integromics and panomics approaches shifted the deciphering of aging mechanisms from single molecular entities to communities of them. In this orientation, we explore the cardiac aging mechanisms – risk factor for multiple cardiovascular diseases - by capturing the micronome synergism and detecting longevity signatures in the form of communities (modules). For this, we developed a meta-analysis scheme that integrates transcriptome expression data from multiple cardiac-specific independent studies in mouse and human along with proteome and micronome interaction data in the form of multiple independent weighted networks. Modularization of each weighted network produced modules, which in turn were further analyzed so as to define consensus modules across datasets that change substantially during lifespan. Also, we established a metric that determines - from the modular perspective - the synergism of microRNA-microRNA interactions as defined by significantly functionally associated targets. Results The meta-analysis provided 40 consensus integromics modules across mouse datasets and revealed microRNA relations with substantial collective action during aging. Three modules were reproducible, based on homology, when mapped against human-derived modules. The respective homologs mainly represent NADH dehydrogenases, ATP synthases, cytochrome oxidases, Ras GTPases and ribosomal proteins. Among various observations, we corroborate to the involvement of miR-34a (included in consensus modules) as proposed recently; yet we report that has no synergistic effect. Moving forward, we determined its age-related neighborhood in which HCN3, a known heart pacemaker channel, was included. Also, miR-125a-5p/-351, miR-200c/-429, miR-106b/-17, miR-363/-92b, miR-181b/-181d, miR-19a/-19b, let-7d/-7f, miR-18a/-18b, miR-128/-27b and miR-106a/-291a-3p pairs exhibited significant synergy and their association to aging and/or cardiovascular diseases is supported in many cases by a disease database and previous studies. On the contrary, we suggest that miR-22 has not substantial impact on heart longevity as proposed recently. Conclusions We revised several proteins and microRNAs recently implicated in cardiac aging and proposed for the first time modules as signatures. The integromics meta-analysis approach can serve as an efficient subvening signature tool for more-oriented better-designed experiments. It can also promote the combinational multi-target microRNA therapy of age-related cardiovascular diseases along the continuum from prevention to detection, diagnosis, treatment and outcome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1256-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Aristidis G Vrahatis
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Department of Computer Engineering and Informatics, University of Patras, Patras, 26500, Greece.
| | - Anastasios Bezerianos
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Singapore Institute for Neurotechnology (SINAPSE), Center of Life Sciences, National University of Singapore, Singapore, 117456, Singapore.
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