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Wei PJ, Bao JJ, Gao Z, Tan JY, Cao RF, Su Y, Zheng CH, Deng L. MEFFGRN: Matrix enhancement and feature fusion-based method for reconstructing the gene regulatory network of epithelioma papulosum cyprini cells by spring viremia of carp virus infection. Comput Biol Med 2024; 179:108835. [PMID: 38996550 DOI: 10.1016/j.compbiomed.2024.108835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/29/2024] [Indexed: 07/14/2024]
Abstract
Gene regulatory networks (GRNs) are crucial for understanding organismal molecular mechanisms and processes. Construction of GRN in the epithelioma papulosum cyprini (EPC) cells of cyprinid fish by spring viremia of carp virus (SVCV) infection helps understand the immune regulatory mechanisms that enhance the survival capabilities of cyprinid fish. Although many computational methods have been used to infer GRNs, specialized approaches for predicting the GRN of EPC cells following SVCV infection are lacking. In addition, most existing methods focus primarily on gene expression features, neglecting the valuable network structural information in known GRNs. In this study, we propose a novel supervised deep neural network, named MEFFGRN (Matrix Enhancement- and Feature Fusion-based method for Gene Regulatory Network inference), to accurately predict the GRN of EPC cells following SVCV infection. MEFFGRN considers both gene expression data and network structure information of known GRN and introduces a matrix enhancement method to address the sparsity issue of known GRN, extracting richer network structure information. To optimize the benefits of CNN (Convolutional Neural Network) in image processing, gene expression and enhanced GRN data were transformed into histogram images for each gene pair respectively. Subsequently, these histograms were separately fed into CNNs for training to obtain the corresponding gene expression and network structural features. Furthermore, a feature fusion mechanism was introduced to comprehensively integrate the gene expression and network structural features. This integration considers the specificity of each feature and their interactive information, resulting in a more comprehensive and precise feature representation during the fusion process. Experimental results from both real-world and benchmark datasets demonstrate that MEFFGRN achieves competitive performance compared with state-of-the-art computational methods. Furthermore, study findings from SVCV-infected EPC cells suggest that MEFFGRN can predict novel gene regulatory relationships.
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Affiliation(s)
- Pi-Jing Wei
- Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Jin-Jin Bao
- Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Zhen Gao
- Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Jing-Yun Tan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Rui-Fen Cao
- Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Yansen Su
- School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Chun-Hou Zheng
- School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.
| | - Li Deng
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, 518055, Guangdong, China.
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2
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Chee FT, Harun S, Mohd Daud K, Sulaiman S, Nor Muhammad NA. Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 189:1-12. [PMID: 38604435 DOI: 10.1016/j.pbiomolbio.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Gene regulatory network (GRN) comprises complicated yet intertwined gene-regulator relationships. Understanding the GRN dynamics will unravel the complexity behind the observed gene expressions. Insect gene regulation is often complicated due to their complex life cycles and diverse ecological adaptations. The main interest of this review is to have an update on the current mathematical modelling methods of GRNs to explain insect science. Several popular GRN architecture models are discussed, together with examples of applications in insect science. In the last part of this review, each model is compared from different aspects, including network scalability, computation complexity, robustness to noise and biological relevancy.
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Affiliation(s)
- Fong Ting Chee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Sarahani Harun
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Kauthar Mohd Daud
- Faculty of Information Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Suhaila Sulaiman
- FGV R&D Sdn Bhd, FGV Innovation Center, PT23417 Lengkuk Teknologi, Bandar Baru Enstek, 71760 Nilai, Negeri Sembilan, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
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3
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Li S, Liu Y, Shen LC, Yan H, Song J, Yu DJ. GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Brief Bioinform 2024; 25:bbad529. [PMID: 38261340 PMCID: PMC10805180 DOI: 10.1093/bib/bbad529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
The recent advances of single-cell RNA sequencing (scRNA-seq) have enabled reliable profiling of gene expression at the single-cell level, providing opportunities for accurate inference of gene regulatory networks (GRNs) on scRNA-seq data. Most methods for inferring GRNs suffer from the inability to eliminate transitive interactions or necessitate expensive computational resources. To address these, we present a novel method, termed GMFGRN, for accurate graph neural network (GNN)-based GRN inference from scRNA-seq data. GMFGRN employs GNN for matrix factorization and learns representative embeddings for genes. For transcription factor-gene pairs, it utilizes the learned embeddings to determine whether they interact with each other. The extensive suite of benchmarking experiments encompassing eight static scRNA-seq datasets alongside several state-of-the-art methods demonstrated mean improvements of 1.9 and 2.5% over the runner-up in area under the receiver operating characteristic curve (AUROC) and area under the precision-recall curve (AUPRC). In addition, across four time-series datasets, maximum enhancements of 2.4 and 1.3% in AUROC and AUPRC were observed in comparison to the runner-up. Moreover, GMFGRN requires significantly less training time and memory consumption, with time and memory consumed <10% compared to the second-best method. These findings underscore the substantial potential of GMFGRN in the inference of GRNs. It is publicly available at https://github.com/Lishuoyy/GMFGRN.
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Affiliation(s)
- Shuo Li
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Yan Liu
- School of information Engineering, Yangzhou University, 196 West Huayang, Yangzhou, 225000, China
| | - Long-Chen Shen
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - He Yan
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
- Monash Data Futures Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
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4
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Zafar A, Wajid B, Shabbir A, Gohar Awan F, Ahsan M, Ahmad S, Wajid I, Anwar F, Mazhar F. Unearthing Insights into Metabolic Syndrome by Linking Drugs, Targets, and Gene Expressions Using Similarity Measures and Graph Theory. Curr Comput Aided Drug Des 2024; 20:773-783. [PMID: 37592790 DOI: 10.2174/1573409920666230817101913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/13/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023]
Abstract
AIMS AND OBJECTIVES Metabolic syndrome (MetS) is a group of metabolic disorders that includes obesity in combination with at least any two of the following conditions, i.e., insulin resistance, high blood pressure, low HDL cholesterol, and high triglycerides level. Treatment of this syndrome is challenging because of the multiple interlinked factors that lead to increased risks of type-2 diabetes and cardiovascular diseases. This study aims to conduct extensive in silico analysis to (i) find central genes that play a pivotal role in MetS and (ii) propose suitable drugs for therapy. Our objective is to first create a drug-disease network and then identify novel genes in the drug-disease network with strong associations to drug targets, which can help in increasing the therapeutical effects of different drugs. In the future, these novel genes can be used to calculate drug synergy and propose new drugs for the effective treatment of MetS. METHODS For this purpose, we (i) investigated associated drugs and pathways for MetS, (ii) employed eight different similarity measures to construct eight gene regulatory networks, (iii) chose an optimal network, where a maximum number of drug targets were central, (iv) determined central genes exhibiting strong associations with these drug targets and associated disease-causing pathways, and lastly (v) employed these candidate genes to propose suitable drugs. RESULTS Our results indicated (i) a novel drug-disease network complex, with (ii) novel genes associated with MetS. CONCLUSION Our developed drug-disease network complex closely represents MetS with associated novel findings and markers for an improved understanding of the disease and suggested therapy.
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Affiliation(s)
- Alwaz Zafar
- Ibn Sina Research & Development Division, Sabz-Qalam, Lahore, 54000, Pakistan
| | - Bilal Wajid
- Ibn Sina Research & Development Division, Sabz-Qalam, Lahore, 54000, Pakistan
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, 54000, Pakistan
| | - Ans Shabbir
- Ibn Sina Research & Development Division, Sabz-Qalam, Lahore, 54000, Pakistan
| | - Fahim Gohar Awan
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, 54000, Pakistan
| | - Momina Ahsan
- Ibn Sina Research & Development Division, Sabz-Qalam, Lahore, 54000, Pakistan
| | - Sarfraz Ahmad
- Ibn Sina Research & Development Division, Sabz-Qalam, Lahore, 54000, Pakistan
| | - Imran Wajid
- Ibn Sina Research & Development Division, Sabz-Qalam, Lahore, 54000, Pakistan
- Department of Social Sciences, Istanbul Commerce University, Istanbul, Turkey
| | - Faria Anwar
- Outpatient Department, Mayo Hospital, Lahore, 54000, Pakistan
| | - Fazeelat Mazhar
- Department of Biomedical, Electrical and System Engineering, University of Bologna, Cesena Campus, Bologna, Italy
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5
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Xu Y, Chen J, Lyu A, Cheung WK, Zhang L. dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data. Brief Bioinform 2022; 23:6720420. [PMID: 36168811 DOI: 10.1093/bib/bbac424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/02/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022] Open
Abstract
Time-course single-cell RNA sequencing (scRNA-seq) data have been widely used to explore dynamic changes in gene expression of transcription factors (TFs) and their target genes. This information is useful to reconstruct cell-type-specific gene regulatory networks (GRNs). However, the existing tools are commonly designed to analyze either time-course bulk gene expression data or static scRNA-seq data via pseudo-time cell ordering. A few methods successfully utilize the information from multiple time points while also considering the characteristics of scRNA-seq data. We proposed dynDeepDRIM, a novel deep learning model to reconstruct GRNs using time-course scRNA-seq data. It represents the joint expression of a gene pair as an image and utilizes the image of the target TF-gene pair and the ones of the potential neighbors to reconstruct GRNs from time-course scRNA-seq data. dynDeepDRIM can effectively remove the transitive TF-gene interactions by considering neighborhood context and model the gene expression dynamics using high-dimensional tensors. We compared dynDeepDRIM with six GRN reconstruction methods on both simulation and four real time-course scRNA-seq data. dynDeepDRIM achieved substantially better performance than the other methods in inferring TF-gene interactions and eliminated the false positives effectively. We also applied dynDeepDRIM to annotate gene functions and found it achieved evidently better performance than the other tools due to considering the neighbor genes.
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Affiliation(s)
- Yu Xu
- Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Jiaxing Chen
- Computer Science and Technology, Division of Science and Technology, BNU-HKBU United International College, Jintong Road, 519087, Zhuhai, China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - William K Cheung
- Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong
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6
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Liu W, Sun X, Yang L, Li K, Yang Y, Fu X. NSCGRN: a network structure control method for gene regulatory network inference. Brief Bioinform 2022; 23:6585392. [PMID: 35554485 DOI: 10.1093/bib/bbac156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 01/18/2023] Open
Abstract
Accurate inference of gene regulatory networks (GRNs) is an essential premise for understanding pathogenesis and curing diseases. Various computational methods have been developed for GRN inference, but the identification of redundant regulation remains a challenge faced by researchers. Although combining global and local topology can identify and reduce redundant regulations, the topologies' specific forms and cooperation modes are unclear and real regulations may be sacrificed. Here, we propose a network structure control method [network-structure-controlling-based GRN inference method (NSCGRN)] that stipulates the global and local topology's specific forms and cooperation mode. The method is carried out in a cooperative mode of 'global topology dominates and local topology refines'. Global topology requires layering and sparseness of the network, and local topology requires consistency of the subgraph association pattern with the network motifs (fan-in, fan-out, cascade and feedforward loop). Specifically, an ordered gene list is obtained by network topology centrality sorting. A Bernaola-Galvan mutation detection algorithm applied to the list gives the hierarchy of GRNs to control the upstream and downstream regulations within the global scope. Finally, four network motifs are integrated into the hierarchy to optimize local complex regulations and form a cooperative mode where global and local topologies play the dominant and refined roles, respectively. NSCGRN is compared with state-of-the-art methods on three different datasets (six networks in total), and it achieves the highest F1 and Matthews correlation coefficient. Experimental results show its unique advantages in GRN inference.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, 411105, China.,School of Computer Science, Xiangtan University, Xiangtan, 411105, China
| | - Xingen Sun
- School of Computer Science, Xiangtan University, Xiangtan, 411105, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, 411105, China
| | - Li Yang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, 411105, China
| | - Kaiwen Li
- Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou, 221116, China
| | - Yu Yang
- School of Computer Science, Xiangtan University, Xiangtan, 411105, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, 411105, China
| | - Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China
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7
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Gao Y, Li J, Zhao L, Hong Y, Shen L, Wang Y, Lin X. Distribution pattern and surface nature-mediated differential effects of hydrophilic and hydrophobic nano-silica on key direct compaction properties of Citri Reticulatae Pericarpium powder by co-processing. POWDER TECHNOL 2022. [DOI: 10.1016/j.powtec.2022.117442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Abstract
In industrial practice, excessive alarms and high alarm rates are mostly generated from unreasonable settings to variable alarm thresholds, which have become the significant causes of impact on operation stability and plant safety. A correlation degree and clustering analysis-based approach was presented to optimize the variable alarm thresholds in this paper. The correlation degrees of variables are first obtained by analyzing correlation relationships among them. Second, the variables are grouped according to the gray correlation coefficients and clustering analysis, given the weight for fault alarm rate (FAR) in each group. An objective function about the FAR, missed alarm rate (MAR), and the maximum acceptable FAR and MAR is then established with variable weight. Eventually, based on an optimization algorithm, the objective function can be optimized for obtaining the optimal alarm threshold. Cases study of the Tennessee Eastman (TE) industrial simulation process and an actual industrial ethylene production process, in comparison to the initial situation, show that the method can effectively reduce FAR according to correlation degrees among variables in the system, and decrease the number of alarms with reduction rates of 40.5% and 35.3%, respectively.
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9
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Chen J, Cheong C, Lan L, Zhou X, Liu J, Lyu A, Cheung WK, Zhang L. DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data. Brief Bioinform 2021; 22:bbab325. [PMID: 34424948 PMCID: PMC8499812 DOI: 10.1093/bib/bbab325] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 01/11/2023] Open
Abstract
Single-cell RNA sequencing has enabled to capture the gene activities at single-cell resolution, thus allowing reconstruction of cell-type-specific gene regulatory networks (GRNs). The available algorithms for reconstructing GRNs are commonly designed for bulk RNA-seq data, and few of them are applicable to analyze scRNA-seq data by dealing with the dropout events and cellular heterogeneity. In this paper, we represent the joint gene expression distribution of a gene pair as an image and propose a novel supervised deep neural network called DeepDRIM which utilizes the image of the target TF-gene pair and the ones of the potential neighbors to reconstruct GRN from scRNA-seq data. Due to the consideration of TF-gene pair's neighborhood context, DeepDRIM can effectively eliminate the false positives caused by transitive gene-gene interactions. We compared DeepDRIM with nine GRN reconstruction algorithms designed for either bulk or single-cell RNA-seq data. It achieves evidently better performance for the scRNA-seq data collected from eight cell lines. The simulated data show that DeepDRIM is robust to the dropout rate, the cell number and the size of the training data. We further applied DeepDRIM to the scRNA-seq gene expression of B cells from the bronchoalveolar lavage fluid of the patients with mild and severe coronavirus disease 2019. We focused on the cell-type-specific GRN alteration and observed targets of TFs that were differentially expressed between the two statuses to be enriched in lysosome, apoptosis, response to decreased oxygen level and microtubule, which had been proved to be associated with coronavirus infection.
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Affiliation(s)
- Jiaxing Chen
- Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong
| | - ChinWang Cheong
- Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong
| | - Liang Lan
- Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong
| | - Xin Zhou
- Department of Biomedical Engineering, Vanderbilt University, Vanderbilt Place Nashville, 37235, TN, USA
| | - Jiming Liu
- Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong
| | - William K Cheung
- Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Hong Kong
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10
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Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol 2021; 17:e1009095. [PMID: 34166361 PMCID: PMC8263068 DOI: 10.1371/journal.pcbi.1009095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 07/07/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
The effectiveness of immune responses depends on the precision of stimulus-responsive gene expression programs. Cells specify which genes to express by activating stimulus-specific combinations of stimulus-induced transcription factors (TFs). Their activities are decoded by a gene regulatory strategy (GRS) associated with each response gene. Here, we examined whether the GRSs of target genes may be inferred from stimulus-response (input-output) datasets, which remains an unresolved model-identifiability challenge. We developed a mechanistic modeling framework and computational workflow to determine the identifiability of all possible combinations of synergistic (AND) or non-synergistic (OR) GRSs involving three transcription factors. Considering different sets of perturbations for stimulus-response studies, we found that two thirds of GRSs are easily distinguishable but that substantially more quantitative data is required to distinguish the remaining third. To enhance the accuracy of the inference with timecourse experimental data, we developed an advanced error model that avoids error overestimates by distinguishing between value and temporal error. Incorporating this error model into a Bayesian framework, we show that GRS models can be identified for individual genes by considering multiple datasets. Our analysis rationalizes the allocation of experimental resources by identifying most informative TF stimulation conditions. Applying this computational workflow to experimental data of immune response genes in macrophages, we found that a much greater fraction of genes are combinatorially controlled than previously reported by considering compensation among transcription factors. Specifically, we revealed that a group of known NFκB target genes may also be regulated by IRF3, which is supported by chromatin immuno-precipitation analysis. Our study provides a computational workflow for designing and interpreting stimulus-response gene expression studies to identify underlying gene regulatory strategies and further a mechanistic understanding.
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Affiliation(s)
- Ning Wang
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
| | - Diane Lefaudeux
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Anup Mazumder
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Jingyi Jessica Li
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Statistics, University of California, Los Angeles, California, United States of America
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
- * E-mail:
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11
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Zhang Y, Chang X, Liu X. Inference of gene regulatory networks using pseudo-time series data. Bioinformatics 2021; 37:2423-2431. [PMID: 33576787 DOI: 10.1093/bioinformatics/btab099] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/18/2021] [Accepted: 02/10/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Inferring gene regulatory networks (GRNs) from high-throughput data is an important and challenging problem in systems biology. Although numerous GRN methods have been developed, most have focused on the verification of the specific data set. However, it is difficult to establish directed topological networks that are both suitable for time-series and non-time-series datasets due to the complexity and diversity of biological networks. RESULTS Here, we proposed a novel method, GNIPLR (Gene networks inference based on projection and lagged regression) to infer GRNs from time-series or non-time-series gene expression data. GNIPLR projected gene data twice using the LASSO projection (LSP) algorithm and the linear projection (LP) approximation to produce a linear and monotonous pseudo-time series, and then determined the direction of regulation in combination with lagged regression analyses. The proposed algorithm was validated using simulated and real biological data. Moreover, we also applied the GNIPLR algorithm to the liver hepatocellular carcinoma (LIHC) and bladder urothelial carcinoma (BLCA) cancer expression datasets. These analyses revealed significantly higher accuracy and AUC values than other popular methods. AVAILABILITY The GNIPLR tool is freely available at https://github.com/zyllluck/GNIPLR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuelei Zhang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310012, China.,Institute of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu, 233030, China.,School of Mathematics and Statistics, Shandong University, Weihai, Shandong, 264209, China
| | - Xiao Chang
- Institute of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu, 233030, China
| | - Xiaoping Liu
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310012, China.,School of Mathematics and Statistics, Shandong University, Weihai, Shandong, 264209, China
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12
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Liu W, Sun X, Peng L, Zhou L, Lin H, Jiang Y. RWRNET: A Gene Regulatory Network Inference Algorithm Using Random Walk With Restart. Front Genet 2020; 11:591461. [PMID: 33101398 PMCID: PMC7545090 DOI: 10.3389/fgene.2020.591461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 11/30/2022] Open
Abstract
Inferring gene regulatory networks from expression data is essential in identifying complex regulatory relationships among genes and revealing the mechanism of certain diseases. Various computation methods have been developed for inferring gene regulatory networks. However, these methods focus on the local topology of the network rather than on the global topology. From network optimisation standpoint, emphasising the global topology of the network also reduces redundant regulatory relationships. In this study, we propose a novel network inference algorithm using Random Walk with Restart (RWRNET) that combines local and global topology relationships. The method first captures the local topology through three elements of random walk and then combines the local topology with the global topology by Random Walk with Restart. The Markov Blanket discovery algorithm is then used to deal with isolated genes. The proposed method is compared with several state-of-the-art methods on the basis of six benchmark datasets. Experimental results demonstrated the effectiveness of the proposed method.
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Affiliation(s)
- Wei Liu
- School of Computer Science, Xiangtan University, Xiangtan, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, China
| | - Xingen Sun
- School of Computer Science, Xiangtan University, Xiangtan, China
| | - Li Peng
- School of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, China
| | - Lili Zhou
- School of Computer Science, Xiangtan University, Xiangtan, China
| | - Hui Lin
- School of Computer Science, Xiangtan University, Xiangtan, China
| | - Yi Jiang
- School of Computer Science, Xiangtan University, Xiangtan, China
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13
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Wu MJ, Gao YL, Liu JX, Zheng CH, Wang J. Integrative Hypergraph Regularization Principal Component Analysis for Sample Clustering and Co-Expression Genes Network Analysis on Multi-Omics Data. IEEE J Biomed Health Inform 2020; 24:1823-1834. [DOI: 10.1109/jbhi.2019.2948456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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A model to simultaneously evaluate the compressibility and compactibility of a powder based on the compression ratio. Int J Pharm 2020; 577:119023. [DOI: 10.1016/j.ijpharm.2020.119023] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/02/2020] [Accepted: 01/05/2020] [Indexed: 11/19/2022]
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15
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Wang H, Lian Y, Li C, Ma Y, Yan Z, Dong C. SIN-KNO: A method of gene regulatory network inference using single-cell transcription and gene knockout data. J Bioinform Comput Biol 2020; 17:1950035. [PMID: 32019417 DOI: 10.1142/s0219720019500355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As a tool of interpreting and analyzing genetic data, gene regulatory network (GRN) could reveal regulatory relationships between genes, proteins, and small molecules, as well as understand physiological activities and functions within biological cells, interact in pathways, and how to make changes in the organism. Traditional GRN research focuses on the analysis of the regulatory relationships through the average of cellular gene expressions. These methods are difficult to identify the cell heterogeneity of gene expression. Existing methods for inferring GRN using single-cell transcriptional data lack expression information when genes reach steady state, and the high dimensionality of single-cell data leads to high temporal and spatial complexity of the algorithm. In order to solve the problem in traditional GRN inference methods, including the lack of cellular heterogeneity information, single-cell data complexity and lack of steady-state information, we propose a method for GRN inference using single-cell transcription and gene knockout data, called SINgle-cell transcription data-KNOckout data (SIN-KNO), which focuses on combining dynamic and steady-state information of regulatory relationship contained in gene expression. Capturing cell heterogeneity information could help understand the gene expression difference in different cells. So, we could observe gene expression changes more accurately. Gene knockout data could observe the gene expression levels at steady-state of all other genes when one gene is knockout. Classifying the genes before analyzing the single-cell data could determine a large number of non-existent regulation, greatly reducing the number of regulation required for inference. In order to show the efficiency, the proposed method has been compared with several typical methods in this area including GENIE3, JUMP3, and SINCERITIES. The results of the evaluation indicate that the proposed method can analyze the diversified information contained in the two types of data, establish a more accurate gene regulation network, and improve the computational efficiency. The method provides a new thinking for dealing with large datasets and high computational complexity of single-cell data in the GRN inference.
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Affiliation(s)
- Huiqing Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Yuanyuan Lian
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Chun Li
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Yue Ma
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Zhiliang Yan
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Chunlin Dong
- Dryland Agriculture Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
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Transcriptome Analysis Reveals the Effect of Long Intergenic Noncoding RNAs on Pig Muscle Growth and Fat Deposition. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2951427. [PMID: 31341893 PMCID: PMC6614983 DOI: 10.1155/2019/2951427] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/01/2019] [Indexed: 01/09/2023]
Abstract
Muscle growth and fat deposition are the two important biological processes in the development of pigs which are closely related to the pig production performance. Long intergenic noncoding RNAs (lincRNAs), with lack of coding potential and the length of at least 200nt, have been extensively studied to play important roles in many biological processes. However, the importance and molecular regulation mechanism of lincRNAs in the process of muscle growth and fat deposition in pigs are still to be further studied comprehensively. In our study, we used the data, including liver, abdominal fat, and longissimus dorsi muscle of 240 days' age of two F2 full-sib female individuals from the white Duroc and Erhualian crossbreed, to identify 581 putative lincRNAs associated with pig muscle growth and fat deposition. The 581 putative lincRNAs shared many common features with other mammalian lincRNAs, such as fewer exons, lower expression levels, and shorter transcript lengths. Cross-tissue comparisons showed that many transcripts were tissue-specific and were involved in the important biological processes in their corresponding tissues. Gene ontology and pathway analysis revealed that many potential target genes (PTGs) of putative lincRNAs were involved in pig muscle growth and fat deposition-related processes, including muscle cell proliferation, lipid metabolism, and fatty acid degradation. In Quantitative Trait Locus (QTLs) analysis, some PTGs were screened from putative lincRNAs, MRPL12 is associated with muscle growth, GCGR and SLC25A10 were associated with fat deposition, and PPP3CA, DPYD, and FGGY were related not only to muscle growth but also to fat deposition. Therefore, it implied that these lincRNAs might participate in the biological processes related to muscle growth or fat deposition through homeostatic regulation of PTGs, but the detailed molecular regulatory mechanisms still needed to be further explored. This study lays the molecular foundation for the in-depth study of the role of lincRNAs in the pig muscle growth and fat deposition and further provides the new molecular markers for understanding the complex biological mechanisms of pig muscle growth and fat deposition.
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17
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Optimal Design of a Carbon Dioxide Separation Process with Market Uncertainty and Waste Reduction. Processes (Basel) 2019. [DOI: 10.3390/pr7060342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The aim of this work is to optimize the conceptual design of an amine-based carbon dioxide (CO2) separation process for Enhanced Oil Recovery (EOR). A systematic approach is applied to predict the economic profitability of the system while reducing the environmental impacts. Firstly, we model the process with UniSim and determine the governing degrees of freedom (DoF) through a sensitivity analysis. Then, we proceed with the formulation of the economic problem, where the employment of econometric models allows us to predict the highest dynamic economic potential (DEP). In the second part, we apply the Waste Reduction (WAR) algorithm to quantify the environmental risks of the studied process. This method is based on the minimization of the potential environmental indicator (PEI) by using the generalization of the Waste Reduction algorithm. Results show that the CO2 separation plant is promising in terms of economic revenues. However, the PEI value indicates that the higher the profitability, the larger the environmental risk. The optimal value of the DEP corresponds to 0.0274 kmol/h and 60 °C, with a plant capacity according to the mole flow rate of the produced acid gas. In addition, the highest environmental risk is observed at the upper bounds of the DoF.
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18
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Shi G, Chen L, Chen G, Zou C, Li J, Li M, Fang C, Li C. Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs. Front Genet 2019; 10:160. [PMID: 30886630 PMCID: PMC6409335 DOI: 10.3389/fgene.2019.00160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/19/2022] Open
Abstract
An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat development. Here, we used published RNA-seq data from subcutaneous adipose tissue of Italian Large White pigs and identified 252 putative lincRNAs, wherein 34 were unannotated. These lincRNAs had relatively shorter length, lower number of exons, and lower expression level compared with protein-coding transcripts. Gene ontology and pathway analysis indicated that the adjacent genes of lincRNAs were involved in lipid metabolism. In addition, differentially expressed lincRNAs (DELs) between low and high backfat thickness pigs were identified. Through the detection of quantitative trait locus (QTL), DELs were mainly located in QTLs related to adipose development. Based on the expression correlation of DEL genes and their differentially expressed potential target genes, we constructed a co-expression network and a potential pathway of DEL's effect on lipid metabolism. Our study identified and analyzed lincRNAs in subcutaneous adipose tissue, and results suggested that lincRNAs may be involved in the regulation of subcutaneous fat development. Our findings provided new insights into the biological function of porcine lincRNAs.
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Affiliation(s)
- Gaoli Shi
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lin Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jingxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Márquez-Olivera M, Juárez-Gracia AG, Hernández-Herrera V, Argüelles-Cruz AJ, López-Yáñez I. System for Face Recognition under Different Facial Expressions Using a New Associative Hybrid Model Amαβ-KNN for People with Visual Impairment or Prosopagnosia. SENSORS (BASEL, SWITZERLAND) 2019; 19:E578. [PMID: 30704082 PMCID: PMC6386895 DOI: 10.3390/s19030578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/30/2018] [Accepted: 01/10/2019] [Indexed: 11/30/2022]
Abstract
Face recognition is a natural skill that a child performs from the first days of life; unfortunately, there are people with visual or neurological problems that prevent the individual from performing the process visually. This work describes a system that integrates Artificial Intelligence which learns the face of the people with whom the user interacts daily. During the study we propose a new hybrid model of Alpha-Beta Associative memories (Amαβ) with Correlation Matrix (CM) and K-Nearest Neighbors (KNN), where the Amαβ-CMKNN was trained with characteristic biometric vectors generated from images of faces from people who present different facial expressions such as happiness, surprise, anger and sadness. To test the performance of the hybrid model, two experiments that differ in the selection of parameters that characterize the face are conducted. The performance of the proposed model was tested in the databases CK+, CAS-PEAL-R1 and Face-MECS (own), which test the Amαβ-CMKNN with faces of subjects of both sexes, different races, facial expressions, poses and environmental conditions. The hybrid model was able to remember 100% of all the faces learned during their training, while in the test in which faces are presented that have variations with respect to those learned the results range from 95.05% in controlled environments and 86.48% in real environments using the proposed integrated system.
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Affiliation(s)
- Moisés Márquez-Olivera
- CICATA Unidad Legaria, Instituto Politécnico Nacional, Av. Legaria No. 694 Col. Irrigación, CDMX 11500 Mexico City, México.
| | - Antonio-Gustavo Juárez-Gracia
- CICATA Unidad Legaria, Instituto Politécnico Nacional, Av. Legaria No. 694 Col. Irrigación, CDMX 11500 Mexico City, México.
| | - Viridiana Hernández-Herrera
- CIITEC, Instituto Politécnico Nacional, Cerrada Cecati s/n Col. Sta. Catarina, Azc., CDMX 02250 Mexico City, México.
| | - Amadeo-José Argüelles-Cruz
- CIC, Instituto Politécnico Nacional, Av. Juan de Dios Bátiz, Esq. Miguel Othón de Mendizábal, Col. Nueva Industrial Vallejo, CDMX 07738 Mexico City, México.
| | - Itzamá López-Yáñez
- CIDETEC, Instituto Politécnico Nacional, Av. Juan de Dios Bátiz, Esq. Miguel Othón de Mendizábal, Col. Nueva Industrial Vallejo, CDMX 07700 Mexico City, México.
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20
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Yang B, Chen Y, Zhang W, Lv J, Bao W, Huang DS. HSCVFNT: Inference of Time-Delayed Gene Regulatory Network Based on Complex-Valued Flexible Neural Tree Model. Int J Mol Sci 2018; 19:E3178. [PMID: 30326663 PMCID: PMC6214043 DOI: 10.3390/ijms19103178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 11/17/2022] Open
Abstract
Gene regulatory network (GRN) inference can understand the growth and development of animals and plants, and reveal the mystery of biology. Many computational approaches have been proposed to infer GRN. However, these inference approaches have hardly met the need of modeling, and the reducing redundancy methods based on individual information theory method have bad universality and stability. To overcome the limitations and shortcomings, this thesis proposes a novel algorithm, named HSCVFNT, to infer gene regulatory network with time-delayed regulations by utilizing a hybrid scoring method and complex-valued flexible neural network (CVFNT). The regulations of each target gene can be obtained by iteratively performing HSCVFNT. For each target gene, the HSCVFNT algorithm utilizes a novel scoring method based on time-delayed mutual information (TDMI), time-delayed maximum information coefficient (TDMIC) and time-delayed correlation coefficient (TDCC), to reduce the redundancy of regulatory relationships and obtain the candidate regulatory factor set. Then, the TDCC method is utilized to create time-delayed gene expression time-series matrix. Finally, a complex-valued flexible neural tree model is proposed to infer the time-delayed regulations of each target gene with the time-delayed time-series matrix. Three real time-series expression datasets from (Save Our Soul) SOS DNA repair system in E. coli and Saccharomyces cerevisiae are utilized to evaluate the performance of the HSCVFNT algorithm. As a result, HSCVFNT obtains outstanding F-scores of 0.923, 0.8 and 0.625 for SOS network and (In vivo Reverse-Engineering and Modeling Assessment) IRMA network inference, respectively, which are 5.5%, 14.3% and 72.2% higher than the best performance of other state-of-the-art GRN inference methods and time-delayed methods.
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Affiliation(s)
- Bin Yang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.
| | - Yuehui Chen
- School of Information Science and Engineering, University of Jinan, Jinan 250002, China.
| | - Wei Zhang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.
| | - Jiaguo Lv
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.
| | - Wenzheng Bao
- School of Computer Science, China University of Mining and Technology, Xuzhou 221000, China.
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, Tongji University, Shanghai 200092, China.
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21
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The Safety of Transnational Imported Second-Hand Cars: A Case Study on Vehicle-to-Vehicle Crashes in Romania. SUSTAINABILITY 2017. [DOI: 10.3390/su9122380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Brain Tissue Responses to Guide Cannula Insertion and Replacement of a Microrecording Electrode with a Definitive DBS Electrode. J Med Biol Eng 2017. [DOI: 10.1007/s40846-017-0328-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Multiple Linear Regression for Reconstruction of Gene Regulatory Networks in Solving Cascade Error Problems. Adv Bioinformatics 2017; 2017:4827171. [PMID: 28250767 PMCID: PMC5303608 DOI: 10.1155/2017/4827171] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/10/2016] [Accepted: 10/19/2016] [Indexed: 11/17/2022] Open
Abstract
Gene regulatory network (GRN) reconstruction is the process of identifying regulatory gene interactions from experimental data through computational analysis. One of the main reasons for the reduced performance of previous GRN methods had been inaccurate prediction of cascade motifs. Cascade error is defined as the wrong prediction of cascade motifs, where an indirect interaction is misinterpreted as a direct interaction. Despite the active research on various GRN prediction methods, the discussion on specific methods to solve problems related to cascade errors is still lacking. In fact, the experiments conducted by the past studies were not specifically geared towards proving the ability of GRN prediction methods in avoiding the occurrences of cascade errors. Hence, this research aims to propose Multiple Linear Regression (MLR) to infer GRN from gene expression data and to avoid wrongly inferring of an indirect interaction (A → B → C) as a direct interaction (A → C). Since the number of observations of the real experiment datasets was far less than the number of predictors, some predictors were eliminated by extracting the random subnetworks from global interaction networks via an established extraction method. In addition, the experiment was extended to assess the effectiveness of MLR in dealing with cascade error by using a novel experimental procedure that had been proposed in this work. The experiment revealed that the number of cascade errors had been very minimal. Apart from that, the Belsley collinearity test proved that multicollinearity did affect the datasets used in this experiment greatly. All the tested subnetworks obtained satisfactory results, with AUROC values above 0.5.
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24
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Liu X, Quan P, Li S, Liu C, Zhao Y, Zhao Y, Fang L. Time dependence of the enhancement effect of chemical enhancers: Molecular mechanisms of enhancing kinetics. J Control Release 2017; 248:33-44. [DOI: 10.1016/j.jconrel.2017.01.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/10/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
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25
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Young WC, Raftery AE, Yeung KY. A posterior probability approach for gene regulatory network inference in genetic perturbation data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2016; 13:1241-1251. [PMID: 27775378 DOI: 10.3934/mbe.2016041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Inferring gene regulatory networks is an important problem in systems biology. However, these networks can be hard to infer from experimental data because of the inherent variability in biological data as well as the large number of genes involved. We propose a fast, simple method for inferring regulatory relationships between genes from knockdown experiments in the NIH LINCS dataset by calculating posterior probabilities, incorporating prior information. We show that the method is able to find previously identified edges from TRANSFAC and JASPAR and discuss the merits and limitations of this approach.
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Affiliation(s)
- William Chad Young
- University of Washington, Department of Statistics, Box 354322, Seattle, WA 98195-4322, United States.
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26
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Zhang B, Cui L, Zhang K. Dosage- and time-dependent antibacterial effect of zinc oxide nanoparticles determined by a highly uniform SERS negating undesired spectral variation. Anal Bioanal Chem 2016; 408:3853-65. [DOI: 10.1007/s00216-016-9478-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 12/30/2022]
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Hernández-Lemus E, Li W, Meyer P. Advances in systems biology--New trends and perspectives. Comput Biol Chem 2015; 59 Pt B:1-2. [PMID: 26364255 DOI: 10.1016/j.compbiolchem.2015.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Department, National Institute of Genomic Medicine (INMEGEN), and Center for Complexity Sciences, National Autonomous University of México (UNAM), Mexico.
| | - Wentian Li
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, USA.
| | - Pablo Meyer
- Translational Systems Biology and Nanobiotechnology Group, IBM T.J. Watson Research Center, USA.
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