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Musilova J, Vafek Z, Puniya BL, Zimmer R, Helikar T, Sedlar K. Augusta: From RNA-Seq to gene regulatory networks and Boolean models. Comput Struct Biotechnol J 2024; 23:783-790. [PMID: 38312198 PMCID: PMC10837063 DOI: 10.1016/j.csbj.2024.01.013] [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: 10/26/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of a GRN inferred from expression data is further refined by predicting transcription factor binding motifs in promoters of regulated genes and by incorporating verified interactions obtained from databases. Moreover, a refined GRN is transformed into a draft BN by searching in the curated model database and setting logical rules to incoming edges of target genes, which can be further manually edited as the model is provided in the SBML file format. The approach is applicable even if information about the organism under study is not available in the databases, which is typically the case for non-model organisms including most microbes. Augusta can be operated from the command line and, thus, is easy to use for automated prediction of models for various genomes. The Augusta package is freely available at github.com/JanaMus/Augusta. Documentation and tutorials are available at augusta.readthedocs.io.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno 61600, Czech Republic
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Zdenek Vafek
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
- Institute of Forensic Engineering, Brno University of Technology, Brno 61200, Czech Republic
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Ralf Zimmer
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Tomas Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno 61600, Czech Republic
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich 80539, Germany
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2
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Schmidt L, Saynisch M, Hoegsbjerg C, Schmidt A, Mackey A, Lackmann JW, Müller S, Koch M, Brachvogel B, Kjaer M, Antczak P, Krüger M. Spatial proteomics of skeletal muscle using thin cryosections reveals metabolic adaptation at the muscle-tendon transition zone. Cell Rep 2024; 43:114374. [PMID: 38900641 DOI: 10.1016/j.celrep.2024.114374] [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: 12/07/2023] [Revised: 04/05/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Morphological studies of skeletal muscle tissue provide insights into the architecture of muscle fibers, the surrounding cells, and the extracellular matrix (ECM). However, a spatial proteomics analysis of the skeletal muscle including the muscle-tendon transition zone is lacking. Here, we prepare cryotome muscle sections of the mouse soleus muscle and measure each slice using short liquid chromatography-mass spectrometry (LC-MS) gradients. We generate 3,000 high-resolution protein profiles that serve as the basis for a network analysis to reveal the complex architecture of the muscle-tendon junction. Among the protein profiles that increase from muscle to tendon, we find proteins related to neuronal activity, fatty acid biosynthesis, and the renin-angiotensin system (RAS). Blocking the RAS in cultured mouse tenocytes using losartan reduces the ECM synthesis. Overall, our analysis of thin cryotome sections provides a spatial proteome of skeletal muscle and reveals that the RAS acts as an additional regulator of the matrix within muscle-tendon junctions.
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Affiliation(s)
- Luisa Schmidt
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Michael Saynisch
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Christian Hoegsbjerg
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Abigail Mackey
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan-Wilm Lackmann
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Stefan Müller
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Michael Kjaer
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philipp Antczak
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
| | - Marcus Krüger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
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Marku M, Pancaldi V. From time-series transcriptomics to gene regulatory networks: A review on inference methods. PLoS Comput Biol 2023; 19:e1011254. [PMID: 37561790 PMCID: PMC10414591 DOI: 10.1371/journal.pcbi.1011254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Abstract
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the ever increasing demand for more accurate and powerful models, the inference problem remains of broad scientific interest. The abstract representation of biological systems through gene regulatory networks represents a powerful method to study such systems, encoding different amounts and types of information. In this review, we summarize the different types of inference algorithms specifically based on time-series transcriptomics, giving an overview of the main applications of gene regulatory networks in computational biology. This review is intended to give an updated reference of regulatory networks inference tools to biologists and researchers new to the topic and guide them in selecting the appropriate inference method that best fits their questions, aims, and experimental data.
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Affiliation(s)
- Malvina Marku
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
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4
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Morello G, La Cognata V, Guarnaccia M, D'Agata V, Cavallaro S. Cracking the Code of Neuronal Cell Fate. Cells 2023; 12:cells12071057. [PMID: 37048129 PMCID: PMC10093029 DOI: 10.3390/cells12071057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Transcriptional regulation is fundamental to most biological processes and reverse-engineering programs can be used to decipher the underlying programs. In this review, we describe how genomics is offering a systems biology-based perspective of the intricate and temporally coordinated transcriptional programs that control neuronal apoptosis and survival. In addition to providing a new standpoint in human pathology focused on the regulatory program, cracking the code of neuronal cell fate may offer innovative therapeutic approaches focused on downstream targets and regulatory networks. Similar to computers, where faults often arise from a software bug, neuronal fate may critically depend on its transcription program. Thus, cracking the code of neuronal life or death may help finding a patch for neurodegeneration and cancer.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Velia D'Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95124 Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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5
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Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1148. [PMID: 36904008 PMCID: PMC10005043 DOI: 10.3390/plants12051148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. Statistically verified time expression profiles give information about significant changes in expressions through time, and genes with highly correlated time expression profiles, which are annotated in the same biological process, are likely to be functionally connected. A method to obtain robust networks of functionally related genes will be useful to understand the complexity of the transcriptome, leading to biologically relevant insights. We present an algorithm to construct gene functional networks for genes annotated in a given biological process or other aspects of interest. We assume that there are genome-wide time expression profiles for a set of representative genotypes of the species of interest. The method is based on the correlation of time expression profiles, bound by a set of thresholds that assure both, a given false discovery rate, and the discard of correlation outliers. The novelty of the method consists in that a gene expression relation must be repeatedly found in a given set of independent genotypes to be considered valid. This automatically discards relations particular to specific genotypes, assuring a network robustness, which can be set a priori. Additionally, we present an algorithm to find transcription factors candidates for regulating hub genes within a network. The algorithms are demonstrated with data from a large experiment studying gene expression during the development of the fruit in a diverse set of chili pepper genotypes. The algorithm is implemented and demonstrated in a new version of the publicly available R package "Salsa" (version 1.0).
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Affiliation(s)
- Alan Flores-Díaz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Christian Escoto-Sandoval
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Felipe Cervantes-Hernández
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - José J. Ordaz-Ortiz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo 83000, Mexico
| | - Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Ana Garcés-Claver
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
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6
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Computational approaches to understand transcription regulation in development. Biochem Soc Trans 2023; 51:1-12. [PMID: 36695505 PMCID: PMC9988001 DOI: 10.1042/bst20210145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/07/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Gene regulatory networks (GRNs) serve as useful abstractions to understand transcriptional dynamics in developmental systems. Computational prediction of GRNs has been successfully applied to genome-wide gene expression measurements with the advent of microarrays and RNA-sequencing. However, these inferred networks are inaccurate and mostly based on correlative rather than causative interactions. In this review, we highlight three approaches that significantly impact GRN inference: (1) moving from one genome-wide functional modality, gene expression, to multi-omics, (2) single cell sequencing, to measure cell type-specific signals and predict context-specific GRNs, and (3) neural networks as flexible models. Together, these experimental and computational developments have the potential to significantly impact the quality of inferred GRNs. Ultimately, accurately modeling the regulatory interactions between transcription factors and their target genes will be essential to understand the role of transcription factors in driving developmental gene expression programs and to derive testable hypotheses for validation.
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Cummins B, Motta FC, Moseley RC, Deckard A, Campione S, Gameiro M, Gedeon T, Mischaikow K, Haase SB. Experimental guidance for discovering genetic networks through hypothesis reduction on time series. PLoS Comput Biol 2022; 18:e1010145. [PMID: 36215333 PMCID: PMC9584434 DOI: 10.1371/journal.pcbi.1010145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/20/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
Large programs of dynamic gene expression, like cell cyles and circadian rhythms, are controlled by a relatively small "core" network of transcription factors and post-translational modifiers, working in concerted mutual regulation. Recent work suggests that system-independent, quantitative features of the dynamics of gene expression can be used to identify core regulators. We introduce an approach of iterative network hypothesis reduction from time-series data in which increasingly complex features of the dynamic expression of individual, pairs, and entire collections of genes are used to infer functional network models that can produce the observed transcriptional program. The culmination of our work is a computational pipeline, Iterative Network Hypothesis Reduction from Temporal Dynamics (Inherent dynamics pipeline), that provides a priority listing of targets for genetic perturbation to experimentally infer network structure. We demonstrate the capability of this integrated computational pipeline on synthetic and yeast cell-cycle data.
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Affiliation(s)
- Breschine Cummins
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
- * E-mail:
| | - Francis C. Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Robert C. Moseley
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Anastasia Deckard
- Geometric Data Analytics, Durham, North Carolina, United States of America
| | - Sophia Campione
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Marcio Gameiro
- Department of Mathematics, Rutgers University, New Brunswick, New Jersey, United States of America
- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Tomáš Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Konstantin Mischaikow
- Department of Mathematics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Steven B. Haase
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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A novel approach GRNTSTE to reconstruct gene regulatory interactions applied to a case study for rat pineal rhythm gene. Sci Rep 2022; 12:10227. [PMID: 35715583 PMCID: PMC9205975 DOI: 10.1038/s41598-022-14903-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/14/2022] [Indexed: 01/13/2023] Open
Abstract
Accurate inference and prediction of gene regulatory network are very important for understanding dynamic cellular processes. The large-scale time series genomics data are helpful to reveal the molecular dynamics and dynamic biological processes of complex biological systems. Firstly, we collected the time series data of the rat pineal gland tissue in the natural state according to a fixed sampling rate, and performed whole-genome sequencing. The large-scale time-series sequencing data set of rat pineal gland was constructed, which includes 480 time points, the time interval between adjacent time points is 3 min, and the sampling period is 24 h. Then, we proposed a new method of constructing gene expression regulatory network, named the gene regulatory network based on time series data and entropy transfer (GRNTSTE) method. The method is based on transfer entropy and large-scale time-series gene expression data to infer the causal regulatory relationship between genes in a data-driven mode. The comparative experiments prove that GRNTSTE has better performance than dynamical gene network inference with ensemble of trees (dynGENIE3) and SCRIBE, and has similar performance to TENET. Meanwhile, we proved that the performance of GRNTSTE is slightly lower than that of SINCERITIES method and better than other gene regulatory network construction methods in BEELINE framework, which is based on the BEELINE data set. Finally, the rat pineal rhythm gene expression regulatory network was constructed by us based on the GRNTSTE method, which provides an important reference for the study of the pineal rhythm mechanism, and is of great significance to the study of the pineal rhythm mechanism.
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Bao W, Lin X, Yang B, Chen B. Gene Regulatory Identification Based on the Novel Hybrid Time-Delayed Method. Front Genet 2022; 13:888786. [PMID: 35664311 PMCID: PMC9161097 DOI: 10.3389/fgene.2022.888786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 11/28/2022] Open
Abstract
Gene regulatory network (GRN) inference with biology data is a difficult and serious issue in the field of system biology. In order to detect the direct associations of GRN more accurately, a novel two-step GRN inference technique based on the time-delayed correlation coefficient (TDCC) and time-delayed complex-valued S-system model (TDCVSS) is proposed. First, a TDCC algorithm is utilized to construct an initial network. Second, a TDCVSS model is utilized to prune the network topology in order to delete false-positive regulatory relationships for each target gene. The complex-valued restricted additive tree and complex-valued differential evolution are proposed to approximate the optimal TDCVSS model. Finally, the overall network could be inferred by integrating the regulations of all target genes. Two real gene expression datasets from E. coli and S. cerevisiae gene networks are utilized to evaluate the performances of our proposed two-step GRN inference algorithm. The results demonstrated that the proposed algorithm could infer GRN more correct than classical methods and time-delayed methods.
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Affiliation(s)
- Wenzheng Bao
- School of Information Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Xiao Lin
- Department of Pharmaceutics, Zaozhuang Municipal Hospital, Zaozhuang, China
- *Correspondence: Xiao Lin,
| | - Bin Yang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, China 277160
| | - Baitong Chen
- Xuzhou Municipal First People’s Hospital, Xuzhou, China
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Emerging Machine Learning Techniques for Modelling Cellular Complex Systems in Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1338:199-208. [PMID: 34973026 DOI: 10.1007/978-3-030-78775-2_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We live in the big data era in the biomedical field, where machine learning has a very important contribution to the interpretation of complex biological processes and diseases, since it has the potential to create predictive models from multidimensional data sets. Part of the application of machine learning in biomedical science is to study and model complex cellular systems such as biological networks. In this context, the study of complex diseases, such as Alzheimer's diseases (AD), benefits from established methodologies of network science and machine learning as they offer algorithmic tools and techniques that can address the limitations and challenges of modeling and studying cellular AD-related networks. In this paper we analyze the opportunities and challenges at the intersection of machine learning and network biology and whether this can affect the biological interpretation and clarification of diseases. Specifically, we focus on GRN techniques which through omics data and the use of machine learning techniques can construct a network that captures all the information at the molecular level for the disease under study. We record the emerging machine learning techniques that are focus on ensemble tree-based techniques in the area of classification and regression. Their potential for unraveling the complexity of model cellular systems in complex diseases, such as AD, offers the opportunity for novel machine learning methodologies to decipher the mechanisms of the various AD processes.
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Deutschmann IM, Lima-Mendez G, Krabberød AK, Raes J, Vallina SM, Faust K, Logares R. Disentangling environmental effects in microbial association networks. MICROBIOME 2021; 9:232. [PMID: 34823593 PMCID: PMC8620190 DOI: 10.1186/s40168-021-01141-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/20/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not. RESULTS We present EnDED (environmentally driven edge detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally driven. The four approaches are sign pattern, overlap, interaction information, and data processing inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e., environmentally driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally driven edges-87% sign pattern and overlap, 67% interaction information, and 44% data processing inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally driven, while individual methods predicted 24.8% (data processing inequality), 25.7% (interaction information), and up to 84.6% (sign pattern as well as overlap). The fraction of environmentally driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors. CONCLUSIONS To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses. Video abstract.
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Affiliation(s)
- Ina Maria Deutschmann
- Institute of Marine Sciences, CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain
| | - Gipsi Lima-Mendez
- Research Unit in Biology of Microorganisms (URBM), University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - Anders K. Krabberød
- Department of Biosciences/Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, p.b. 1066 Blindern, N-0316 Oslo, Norway
| | - Jeroen Raes
- VIB Center for Microbiology, Herestraat 49-1028, 3000 Leuven, Belgium
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Herestraat 49, 3000 Leuven, Belgium
| | - Sergio M. Vallina
- Spanish Institute of Oceanography (IEO - CSIC), Ave Principe de Asturias 70 Bis, 33212 Gijon, Spain
| | - Karoline Faust
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Herestraat 49, 3000 Leuven, Belgium
| | - Ramiro Logares
- Institute of Marine Sciences, CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain
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Biswas S, Acharyya S. Multi-objective Simulated Annealing Variants to Infer Gene Regulatory Network: A Comparative Study. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2612-2623. [PMID: 32386161 DOI: 10.1109/tcbb.2020.2992304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene Regulatory Network (GRN) is formed due to mutual transcriptional regulation within a set of protein coding genes in cellular context of an organism. Computational inference of GRN is important to understand the behavior of each gene in terms of change in its protein production rate (expression level). As Recurrent Neural Network (RNN) is efficient in GRN modeling, a bi-objective RNN formulation has been applied here. Based on Archived Multi Objective Simulated Annealing (AMOSA), four algorithms, namely, AMOSA Revised (AMOSAR), Modified Freezing based AMOSA (AMOFSA), Tabu based AMOSA (AMOTSA) and Modified Freezing and Tabu based AMOSA (AMOFTSA) have been proposed and applied to RNN (treated as GRN) for parameter learning taking four gene expression time series datasets. Comparative studies on the performance of the algorithms (based on each dataset) have been made in terms of the number of GRNs obtained in the final non-dominated front and the performance metrics, namely, recall, precision and f1 score. Two proposed variants, namely, AMOFSA and AMOTSA have been found competitive in performance. Experimental observations and statistical analysis show that, modified algorithms are better than AMOSAR and the state-of-the-art algorithms in respect of the above-mentioned metrics.
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13
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Gabor A, Tognetti M, Driessen A, Tanevski J, Guo B, Cao W, Shen H, Yu T, Chung V, Bodenmiller B, Saez‐Rodriguez J. Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd. Mol Syst Biol 2021; 17:e10402. [PMID: 34661974 PMCID: PMC8522707 DOI: 10.15252/msb.202110402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/30/2022] Open
Abstract
Recent technological developments allow us to measure the status of dozens of proteins in individual cells. This opens the way to understand the heterogeneity of complex multi-signaling networks across cells and cell types, with important implications to understand and treat diseases such as cancer. These technologies are, however, limited to proteins for which antibodies are available and are fairly costly, making predictions of new markers and of existing markers under new conditions a valuable alternative. To assess our capacity to make such predictions and boost further methodological development, we organized the Single Cell Signaling in Breast Cancer DREAM challenge. We used a mass cytometry dataset, covering 36 markers in over 4,000 conditions totaling 80 million single cells across 67 breast cancer cell lines. Through four increasingly difficult subchallenges, the participants predicted missing markers, new conditions, and the time-course response of single cells to stimuli in the presence and absence of kinase inhibitors. The challenge results show that despite the stochastic nature of signal transduction in single cells, the signaling events are tightly controlled and machine learning methods can accurately predict new experimental data.
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Affiliation(s)
- Attila Gabor
- Institute for Computational BiomedicineHeidelberg University and Heidelberg University HospitalFaculty of MedicineBioquantHeidelbergGermany
| | - Marco Tognetti
- Department of Quantitative Biomedicine & Institute of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Molecular Life Science PhD ProgramLife Science Zurich Graduate SchoolETH Zurich and University of ZurichZurichSwitzerland
| | - Alice Driessen
- Institute for Computational BiomedicineHeidelberg University and Heidelberg University HospitalFaculty of MedicineBioquantHeidelbergGermany
| | - Jovan Tanevski
- Institute for Computational BiomedicineHeidelberg University and Heidelberg University HospitalFaculty of MedicineBioquantHeidelbergGermany
| | - Baosen Guo
- Division of AI & BioinformaticsShenzhen Digital Life InstituteShenzhenChina
| | - Wencai Cao
- Division of AI & BioinformaticsShenzhen Digital Life InstituteShenzhenChina
| | - He Shen
- Division of AI & BioinformaticsShenzhen Digital Life InstituteShenzhenChina
| | | | | | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine & Institute of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Julio Saez‐Rodriguez
- Institute for Computational BiomedicineHeidelberg University and Heidelberg University HospitalFaculty of MedicineBioquantHeidelbergGermany
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14
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Yang B, Bao W, Zhang W, Wang H, Song C, Chen Y, Jiang X. Reverse engineering gene regulatory network based on complex-valued ordinary differential equation model. BMC Bioinformatics 2021; 22:448. [PMID: 34544363 PMCID: PMC8451084 DOI: 10.1186/s12859-021-04367-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The growing researches of molecular biology reveal that complex life phenomena have the ability to demonstrating various types of interactions in the level of genomics. To establish the interactions between genes or proteins and understand the intrinsic mechanisms of biological systems have become an urgent need and study hotspot. RESULTS In order to forecast gene expression data and identify more accurate gene regulatory network, complex-valued version of ordinary differential equation (CVODE) is proposed in this paper. In order to optimize CVODE model, a complex-valued hybrid evolutionary method based on Grammar-guided genetic programming and complex-valued firefly algorithm is presented. CONCLUSIONS When tested on three real gene expression datasets from E. coli and Human Cell, the experiment results suggest that CVODE model could improve 20-50% prediction accuracy of gene expression data, which could also infer more true-positive regulatory relationships and less false-positive regulations than ordinary differential equation.
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Affiliation(s)
- Bin Yang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China
| | - Wenzheng Bao
- School of Information and Electrical Engineering, Xuzhou University of Technology, Xuzhou, 221018, China.
| | - Wei Zhang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China
| | - Haifeng Wang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China
| | - Chuandong Song
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China
| | - Yuehui Chen
- School of Information Science and Engineering, University of Jinan, Jinan, 250022, China
| | - Xiuying Jiang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China
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15
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Nudelman I, Kudrin D, Nudelman G, Deshpande R, Hartmann BM, Kleinstein SH, Myers CL, Sealfon SC, Zaslavsky E. Comparing Host Module Activation Patterns and Temporal Dynamics in Infection by Influenza H1N1 Viruses. Front Immunol 2021; 12:691758. [PMID: 34335598 PMCID: PMC8317020 DOI: 10.3389/fimmu.2021.691758] [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: 04/07/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Influenza is a serious global health threat that shows varying pathogenicity among different virus strains. Understanding similarities and differences among activated functional pathways in the host responses can help elucidate therapeutic targets responsible for pathogenesis. To compare the types and timing of functional modules activated in host cells by four influenza viruses of varying pathogenicity, we developed a new DYNAmic MOdule (DYNAMO) method that addresses the need to compare functional module utilization over time. This integrative approach overlays whole genome time series expression data onto an immune-specific functional network, and extracts conserved modules exhibiting either different temporal patterns or overall transcriptional activity. We identified a common core response to influenza virus infection that is temporally shifted for different viruses. We also identified differentially regulated functional modules that reveal unique elements of responses to different virus strains. Our work highlights the usefulness of combining time series gene expression data with a functional interaction map to capture temporal dynamics of the same cellular pathways under different conditions. Our results help elucidate conservation of the immune response both globally and at a granular level, and provide mechanistic insight into the differences in the host response to infection by influenza strains of varying pathogenicity.
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Affiliation(s)
- Irina Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Division of General Internal Medicine, New York University Langone Medical Centre, New York, NY, United States
| | - Daniil Kudrin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Boris M Hartmann
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN, United States.,Program in Biomedical Informatics and Computational Biology, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
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16
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Kronberg J, Byrne JJ, Jansen J, Antczak P, Hines A, Bignell J, Katsiadaki I, Viant MR, Falciani F. Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site. Sci Rep 2021; 11:12882. [PMID: 34145300 PMCID: PMC8213754 DOI: 10.1038/s41598-021-90494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022] Open
Abstract
The monitoring of anthropogenic chemicals in the aquatic environment including their potential effects on aquatic organisms, is important for protecting life under water, a key sustainable development goal. In parallel with monitoring the concentrations of chemicals of concern, sentinel species are often used to investigate the biological effects of contaminants. Among these, bivalve molluscs such as mussels are filter-feeding and sessile, hence an excellent model system for measuring localized pollution. This study investigates the relationship between the metabolic state of the blue mussel (Mytilus edulis) and its physiology in different environments. We developed a computational model based on a reference site (relatively unpolluted) and integrated seasonal dynamics of metabolite relative concentrations with key physiological indicators and environmental parameters. The analysis of the model revealed that changes in metabolite levels during an annual cycle are influenced by water temperature and are linked to gonadal development. This work supports the importance of data-driven biology and its potential in environmental monitoring.
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Affiliation(s)
- Jaanika Kronberg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK.,Estonian Genome Centre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jonathan J Byrne
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Philipp Antczak
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Adam Hines
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - John Bignell
- Centre for Environment Fisheries and Aquaculture Science (Cefas), The North, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Ioanna Katsiadaki
- Centre for Environment Fisheries and Aquaculture Science (Cefas), The North, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Francesco Falciani
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK.
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17
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Oh VKS, Li RW. Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data. Genes (Basel) 2021; 12:352. [PMID: 33673721 PMCID: PMC7997275 DOI: 10.3390/genes12030352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Dynamic studies in time course experimental designs and clinical approaches have been widely used by the biomedical community. These applications are particularly relevant in stimuli-response models under environmental conditions, characterization of gradient biological processes in developmental biology, identification of therapeutic effects in clinical trials, disease progressive models, cell-cycle, and circadian periodicity. Despite their feasibility and popularity, sophisticated dynamic methods that are well validated in large-scale comparative studies, in terms of statistical and computational rigor, are less benchmarked, comparing to their static counterparts. To date, a number of novel methods in bulk RNA-Seq data have been developed for the various time-dependent stimuli, circadian rhythms, cell-lineage in differentiation, and disease progression. Here, we comprehensively review a key set of representative dynamic strategies and discuss current issues associated with the detection of dynamically changing genes. We also provide recommendations for future directions for studying non-periodical, periodical time course data, and meta-dynamic datasets.
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Affiliation(s)
- Vera-Khlara S. Oh
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
- Department of Computer Science and Statistics, College of Natural Sciences, Jeju National University, Jeju City 63243, Korea
| | - Robert W. Li
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
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18
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Cheung FKM, Qin J. The Methods and Tools for Molecular Network Construction. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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19
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20
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Lu J, Dumitrascu B, McDowell IC, Jo B, Barrera A, Hong LK, Leichter SM, Reddy TE, Engelhardt BE. Causal network inference from gene transcriptional time-series response to glucocorticoids. PLoS Comput Biol 2021; 17:e1008223. [PMID: 33513136 PMCID: PMC7875426 DOI: 10.1371/journal.pcbi.1008223] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/10/2021] [Accepted: 08/07/2020] [Indexed: 11/19/2022] Open
Abstract
Gene regulatory network inference is essential to uncover complex relationships among gene pathways and inform downstream experiments, ultimately enabling regulatory network re-engineering. Network inference from transcriptional time-series data requires accurate, interpretable, and efficient determination of causal relationships among thousands of genes. Here, we develop Bootstrap Elastic net regression from Time Series (BETS), a statistical framework based on Granger causality for the recovery of a directed gene network from transcriptional time-series data. BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. BETS is highly parallelized, enabling efficient analysis of large transcriptional data sets. We show competitive accuracy on a community benchmark, the DREAM4 100-gene network inference challenge, where BETS is one of the fastest among methods of similar performance and additionally infers whether causal effects are activating or inhibitory. We apply BETS to transcriptional time-series data of differentially-expressed genes from A549 cells exposed to glucocorticoids over a period of 12 hours. We identify a network of 2768 genes and 31,945 directed edges (FDR ≤ 0.2). We validate inferred causal network edges using two external data sources: Overexpression experiments on the same glucocorticoid system, and genetic variants associated with inferred edges in primary lung tissue in the Genotype-Tissue Expression (GTEx) v6 project. BETS is available as an open source software package at https://github.com/lujonathanh/BETS.
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Affiliation(s)
- Jonathan Lu
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| | - Bianca Dumitrascu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Ian C. McDowell
- Element Genomics, A UCB Company, Durham, North Carolina, United States of America
| | - Brian Jo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Alejandro Barrera
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Linda K. Hong
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Sarah M. Leichter
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Timothy E. Reddy
- Department of Genome Sciences, Duke University, Durham, North Carolina, United States of America
| | - Barbara E. Engelhardt
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey, United States of America
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21
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Tang Z, Chai X, Wang Y, Cao S. Gene Regulatory Network Construction Based on a Particle Swarm Optimization of a Long Short-term Memory Network. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191023115224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The Gene Regulatory Network (GRN) is a model for studying the
function and behavior of genes by treating the genome as a whole, which can reveal the gene
expression mechanism. However, due to the dynamics, nonlinearity, and complexity of gene
expression data, it is a challenging task to construct a GRN precisely. And in the circulating
cooling water system, the Slime-Forming Bacteria (SFB) is one of the bacteria that helps to form
dirt. In order to explore the microbial fouling mechanism of SFB, constructing a GRN for the
fouling-forming genes of SFB is significant.
Objective:
Propose an effective GRN construction method and construct a GRN for the foulingforming
genes of SFB.
Methods:
In this paper, a combination method of Long Short-Term Memory Network (LSTM) and
Mean Impact Value (MIV) was applied for GRN reconstruction. Firstly, LSTM was employed to
establish a gene expression prediction model. To improve the performance of LSTM, a Particle
Swarm Optimization (PSO) was introduced to optimize the weight and learning rate. Then, the
MIV was used to infer the regulation among genes. In view of the fouling-forming problem of
SFB, we have designed electromagnetic field experiments and transcriptome sequencing
experiments to locate the fouling-forming genes and obtain gene expression data.
Results:
In order to test the proposed approach, the proposed method was applied to three datasets:
a simulated dataset and two real biology datasets. By comparing with other methods, the
experimental results indicate that the proposed method has higher modeling accuracy and it can be
used to effectively construct a GRN. And at last, a GRN for fouling-forming genes of SFB was
constructed using the proposed approach.
Conclusion:
The experiments indicated that the proposed approach can reconstruct a GRN
precisely, and compared with other approaches, the proposed approach performs better in
extracting the regulations among genes.
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Affiliation(s)
- Zhenhao Tang
- School of Automation Engineering, Northeast Electric Power University, Jilin, China
| | - Xiangying Chai
- School of Automation Engineering, Northeast Electric Power University, Jilin, China
| | - Yu Wang
- School of Automation Engineering, Northeast Electric Power University, Jilin, China
| | - Shengxian Cao
- School of Automation Engineering, Northeast Electric Power University, Jilin, China
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22
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Abstract
OBJECTIVES Numerous software has been developed to infer the gene regulatory network, a long-standing key topic in biology and computational biology. Yet the slowness and inaccuracy inherited in current software hamper their applications to the increasing massive data. Here, we develop a software, FINET (Fast Inferring NETwork), to infer a network with high accuracy and rapidity from big data. RESULTS The high accuracy results from integrating algorithms with stability-selection, elastic-net, and parameter optimization. Tested by a known biological network, FINET infers interactions with over 94% precision. The high speed comes from partnering parallel computations implemented with Julia, a new compiled language that runs much faster than existing languages used in the current software, such as R, Python, and MATLAB. Regardless of FINET's implementations with Julia, users with no background in the language or computer science can easily operate it, with only a user-friendly single command line. In addition, FINET can infer other networks such as chemical networks and social networks. Overall, FINET provides a confident way to efficiently and accurately infer any type of network for any scale of data.
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Affiliation(s)
- Anyou Wang
- The Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA.
| | - Rong Hai
- The Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA. .,Department of Microbiology and Plant Pathology, University of California at Riverside, Riverside, CA, 92521, USA.
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23
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Kwon MS, Lee BT, Lee SY, Kim HU. Modeling regulatory networks using machine learning for systems metabolic engineering. Curr Opin Biotechnol 2020; 65:163-170. [DOI: 10.1016/j.copbio.2020.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022]
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24
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Che D, Guo S, Jiang Q, Chen L. PFBNet: a priori-fused boosting method for gene regulatory network inference. BMC Bioinformatics 2020; 21:308. [PMID: 32664870 PMCID: PMC7362553 DOI: 10.1186/s12859-020-03639-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of potential interactions. RESULTS We present a novel method, namely priori-fused boosting network inference method (PFBNet), to infer GRNs from time-series expression data by using the non-linear model of Boosting and the prior information (e.g., the knockout data) fusion scheme. Specifically, PFBNet first calculates the confidences of the regulation relationships using the boosting-based model, where the information about the accumulation impact of the gene expressions at previous time points is taken into account. Then, a newly defined strategy is applied to fuse the information from the prior data by elevating the confidences of the regulation relationships from the corresponding regulators. CONCLUSIONS The experiments on the benchmark datasets from DREAM challenge as well as the E.coli datasets show that PFBNet achieves significantly better performance than other state-of-the-art methods (Jump3, GEINE3-lag, HiDi, iRafNet and BiXGBoost).
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Affiliation(s)
- Dandan Che
- Shenzhen Key Lab for High Performance Data Mining, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000 China
| | - Shun Guo
- Shenzhen Key Lab for High Performance Data Mining, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000 China
| | - Qingshan Jiang
- Shenzhen Key Lab for High Performance Data Mining, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000 China
| | - Lifei Chen
- School of Mathematics and Computer Science, Fujian Normal University, Fujian, 350117 China
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25
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Gene regulatory network inference from sparsely sampled noisy data. Nat Commun 2020; 11:3493. [PMID: 32661225 PMCID: PMC7359369 DOI: 10.1038/s41467-020-17217-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 06/11/2020] [Indexed: 12/16/2022] Open
Abstract
The complexity of biological systems is encoded in gene regulatory networks. Unravelling this intricate web is a fundamental step in understanding the mechanisms of life and eventually developing efficient therapies to treat and cure diseases. The major obstacle in inferring gene regulatory networks is the lack of data. While time series data are nowadays widely available, they are typically noisy, with low sampling frequency and overall small number of samples. This paper develops a method called BINGO to specifically deal with these issues. Benchmarked with both real and simulated time-series data covering many different gene regulatory networks, BINGO clearly and consistently outperforms state-of-the-art methods. The novelty of BINGO lies in a nonparametric approach featuring statistical sampling of continuous gene expression profiles. BINGO's superior performance and ease of use, even by non-specialists, make gene regulatory network inference available to any researcher, helping to decipher the complex mechanisms of life.
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26
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Finkle JD, Bagheri N. Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights. Bioinformatics 2020; 35:4671-4678. [PMID: 30994899 PMCID: PMC6853664 DOI: 10.1093/bioinformatics/btz256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/07/2019] [Accepted: 04/11/2019] [Indexed: 12/02/2022] Open
Abstract
Motivation To understand the regulatory pathways underlying diseases, studies often investigate the differential gene expression between genetically or chemically differing cell populations. Differential expression analysis identifies global changes in transcription and enables the inference of functional roles of applied perturbations. This approach has transformed the discovery of genetic drivers of disease and possible therapies. However, differential expression analysis does not provide quantitative predictions of gene expression in untested conditions. We present a hybrid approach, termed Differential Expression in Python (DiffExPy), that uniquely combines discrete, differential expression analysis with in silico differential equation simulations to yield accurate, quantitative predictions of gene expression from time-series data. Results To demonstrate the distinct insight provided by DiffExpy, we applied it to published, in vitro, time-series RNA-seq data from several genetic PI3K/PTEN variants of MCF10a cells stimulated with epidermal growth factor. DiffExPy proposed ensembles of several minimal differential equation systems for each differentially expressed gene. These systems provide quantitative models of expression for several previously uncharacterized genes and uncover new regulation by the PI3K/PTEN pathways. We validated model predictions on expression data from conditions that were not used for model training. Our discrete, differential expression analysis also identified SUZ12 and FOXA1 as possible regulators of specific groups of genes that exhibit late changes in expression. Our work reveals how DiffExPy generates quantitatively predictive models with testable, biological hypotheses from time-series expression data. Availability and implementation DiffExPy is available on GitHub (https://github.com/bagherilab/diffexpy). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justin D Finkle
- Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Neda Bagheri
- Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL 60208, USA.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes, Northwestern University, Evanston, IL 60208, USA
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27
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Abstract
Gene regulatory network inference is one of the central problems in computational biology. We need models that integrate the variety of data available in order to use their complementarity information to overcome the issues of noisy and limited data. BENIN: Biologically Enhanced Network INference is our proposal to integrate data and infer more accurate networks. BENIN is a general framework that jointly considers different types of prior knowledge with expression datasets to improve the network inference. The method states the network inference as a feature selection problem and uses a popular penalized regression method, the Elastic net, combined with bootstrap resampling to solve it. BENIN significantly outperforms the state-of-the-art methods on the simulated data from the DREAM 4 challenge when combining genome-wide location data, knockout gene expression data, and time series expression data.
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Affiliation(s)
- Stephanie Kamgnia Wonkap
- Computer Science and Software Engineering, Concordia University, 1455 Boulevard de Maisonneuve Ouest, Montreal, Quebec H3G1M8, Canada
| | - Gregory Butler
- Computer Science and Software Engineering, Concordia University, 1455 Boulevard de Maisonneuve Ouest, Montreal, Quebec H3G1M8, Canada
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28
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Chanda P, Costa E, Hu J, Sukumar S, Van Hemert J, Walia R. Information Theory in Computational Biology: Where We Stand Today. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E627. [PMID: 33286399 PMCID: PMC7517167 DOI: 10.3390/e22060627] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 12/30/2022]
Abstract
"A Mathematical Theory of Communication" was published in 1948 by Claude Shannon to address the problems in the field of data compression and communication over (noisy) communication channels. Since then, the concepts and ideas developed in Shannon's work have formed the basis of information theory, a cornerstone of statistical learning and inference, and has been playing a key role in disciplines such as physics and thermodynamics, probability and statistics, computational sciences and biological sciences. In this article we review the basic information theory based concepts and describe their key applications in multiple major areas of research in computational biology-gene expression and transcriptomics, alignment-free sequence comparison, sequencing and error correction, genome-wide disease-gene association mapping, metabolic networks and metabolomics, and protein sequence, structure and interaction analysis.
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Affiliation(s)
- Pritam Chanda
- Corteva Agriscience™, Indianapolis, IN 46268, USA
- Computer and Information Science, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Eduardo Costa
- Corteva Agriscience™, Mogi Mirim, Sao Paulo 13801-540, Brazil
| | - Jie Hu
- Corteva Agriscience™, Indianapolis, IN 46268, USA
| | | | | | - Rasna Walia
- Corteva Agriscience™, Johnston, IA 50131, USA
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Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM. Gene regulatory network inference resources: A practical overview. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194430. [PMID: 31678629 DOI: 10.1016/j.bbagrm.2019.194430] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional regulation is a fundamental molecular mechanism involved in almost every aspect of life, from homeostasis to development, from metabolism to behavior, from reaction to stimuli to disease progression. In recent years, the concept of Gene Regulatory Networks (GRNs) has grown popular as an effective applied biology approach for describing the complex and highly dynamic set of transcriptional interactions, due to its easy-to-interpret features. Since cataloguing, predicting and understanding every GRN connection in all species and cellular contexts remains a great challenge for biology, researchers have developed numerous tools and methods to infer regulatory processes. In this review, we catalogue these methods in six major areas, based on the dominant underlying information leveraged to infer GRNs: Coexpression, Sequence Motifs, Chromatin Immunoprecipitation (ChIP), Orthology, Literature and Protein-Protein Interaction (PPI) specifically focused on transcriptional complexes. The methods described here cover a wide range of user-friendliness: from web tools that require no prior computational expertise to command line programs and algorithms for large scale GRN inferences. Each method for GRN inference described herein effectively illustrates a type of transcriptional relationship, with many methods being complementary to others. While a truly holistic approach for inferring and displaying GRNs remains one of the greatest challenges in the field of systems biology, we believe that the integration of multiple methods described herein provides an effective means with which experimental and computational biologists alike may obtain the most complete pictures of transcriptional relationships. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Laura Scalambra
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luca Triboli
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Forest Ray
- Department of Systems Biology, Columbia University Medical Center, New York, NY, United States
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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Wani N, Raza K. Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods. Comput Biol Chem 2019; 83:107120. [PMID: 31499298 DOI: 10.1016/j.compbiolchem.2019.107120] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/22/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data. These data have different types (discrete, real, string, etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data (copy number variation, single nucleotide polymorphisms), annotations, interactions, and association data are some of the commonly used biological datasets to study various cellular mechanisms of living organisms. Each of them provides a unique, complementary and partly independent view of the genome and hence embed essential information about the regulatory mechanisms of genes and their products. Therefore, integrating these data and inferring regulatory interactions from them offer a system level of biological insight in predicting gene functions and their phenotypic outcomes. To study genome functionality through regulatory networks, different methods have been proposed for collective mining of information from an integrated dataset. We survey here integration methods that reconstruct regulatory networks using state-of-the-art techniques to handle multi-omics (i.e., genomic, transcriptomic, proteomic) and other biological datasets.
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Affiliation(s)
- Nisar Wani
- Govt. Degree College Baramulla, J & K, India; Department of Computer Science, jamia Milia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, jamia Milia Islamia, New Delhi, India.
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31
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Yan J, Risacher SL, Shen L, Saykin AJ. Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. Brief Bioinform 2019; 19:1370-1381. [PMID: 28679163 DOI: 10.1093/bib/bbx066] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 11/14/2022] Open
Abstract
In the past decade, significant progress has been made in complex disease research across multiple omics layers from genome, transcriptome and proteome to metabolome. There is an increasing awareness of the importance of biological interconnections, and much success has been achieved using systems biology approaches. However, because of the typical focus on one single omics layer at a time, existing systems biology findings explain only a modest portion of complex disease. Recent advances in multi-omics data collection and sharing present us new opportunities for studying complex diseases in a more comprehensive fashion, and yet simultaneously create new challenges considering the unprecedented data dimensionality and diversity. Here, our goal is to review extant and emerging network approaches that can be applied across multiple biological layers to facilitate a more comprehensive and integrative multilayered omics analysis of complex diseases.
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Affiliation(s)
- Jingwen Yan
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, USA
| | - Li Shen
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, USA
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32
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Chan TE, Stumpf MPH, Babtie AC. Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures. Cell Syst 2019; 5:251-267.e3. [PMID: 28957658 PMCID: PMC5624513 DOI: 10.1016/j.cels.2017.08.014] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 04/26/2017] [Accepted: 08/24/2017] [Indexed: 12/03/2022]
Abstract
While single-cell gene expression experiments present new challenges for data processing, the cell-to-cell variability observed also reveals statistical relationships that can be used by information theory. Here, we use multivariate information theory to explore the statistical dependencies between triplets of genes in single-cell gene expression datasets. We develop PIDC, a fast, efficient algorithm that uses partial information decomposition (PID) to identify regulatory relationships between genes. We thoroughly evaluate the performance of our algorithm and demonstrate that the higher-order information captured by PIDC allows it to outperform pairwise mutual information-based algorithms when recovering true relationships present in simulated data. We also infer gene regulatory networks from three experimental single-cell datasets and illustrate how network context, choices made during analysis, and sources of variability affect network inference. PIDC tutorials and open-source software for estimating PID are available. PIDC should facilitate the identification of putative functional relationships and mechanistic hypotheses from single-cell transcriptomic data. PIDC infers gene regulatory networks from single-cell transcriptomic data Multivariate information measures and context in PIDC improve network inference Heterogeneity in single-cell data carries information about gene-gene interactions Fast, efficient, open-source software is made freely available
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Affiliation(s)
- Thalia E Chan
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Michael P H Stumpf
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; MRC London Institute of Medical Sciences, Hammersmith Campus, Imperial College London, London W12 0NN, UK.
| | - Ann C Babtie
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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Ahn H, Jo K, Jeong D, Pak M, Hur J, Jung W, Kim S. PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. FRONTIERS IN PLANT SCIENCE 2019; 10:698. [PMID: 31258543 PMCID: PMC6587906 DOI: 10.3389/fpls.2019.00698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Transcription factor (TF) has a significant influence on the state of a cell by regulating multiple down-stream genes. Thus, experimental and computational biologists have made great efforts to construct TF gene networks for regulatory interactions between TFs and their target genes. Now, an important research question is how to utilize TF networks to investigate the response of a plant to stress at the transcription control level using time-series transcriptome data. In this article, we present a new computational network, PropaNet, to investigate dynamics of TF networks from time-series transcriptome data using two state-of-the-art network analysis techniques, influence maximization and network propagation. PropaNet uses the influence maximization technique to produce a ranked list of TFs, in the order of TF that explains differentially expressed genes (DEGs) better at each time point. Then, a network propagation technique is used to select a group of TFs that explains DEGs best as a whole. For the analysis of Arabidopsis time series datasets from AtGenExpress, we used PlantRegMap as a template TF network and performed PropaNet analysis to investigate transcriptional dynamics of Arabidopsis under cold and heat stress. The time varying TF networks showed that Arabidopsis responded to cold and heat stress quite differently. For cold stress, bHLH and bZIP type TFs were the first responding TFs and the cold signal influenced histone variants, various genes involved in cell architecture, osmosis and restructuring of cells. However, the consequences of plants under heat stress were up-regulation of genes related to accelerating differentiation and starting re-differentiation. In terms of energy metabolism, plants under heat stress show elevated metabolic process and resulting in an exhausted status. We believe that PropaNet will be useful for the construction of condition-specific time-varying TF network for time-series data analysis in response to stress. PropaNet is available at http://biohealth.snu.ac.kr/software/PropaNet.
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Affiliation(s)
- Hongryul Ahn
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
| | - Kyuri Jo
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Minwoo Pak
- Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea
| | - Jihye Hur
- Department of Crop Science, Konkuk University, Seoul, South Korea
| | - Woosuk Jung
- Department of Crop Science, Konkuk University, Seoul, South Korea
| | - Sun Kim
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea
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Kizhakkethil Youseph AS, Chetty M, Karmakar G. Reverse engineering genetic networks using nonlinear saturation kinetics. Biosystems 2019; 182:30-41. [PMID: 31185246 DOI: 10.1016/j.biosystems.2019.103977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/25/2019] [Accepted: 05/27/2019] [Indexed: 01/01/2023]
Abstract
A gene regulatory network (GRN) represents a set of genes along with their regulatory interactions. Cellular behavior is driven by genetic level interactions. Dynamics of such systems show nonlinear saturation kinetics which can be best modeled by Michaelis-Menten (MM) and Hill equations. Although MM equation is being widely used for modeling biochemical processes, it has been applied rarely for reverse engineering GRNs. In this paper, we develop a complete framework for a novel model for GRN inference using MM kinetics. A set of coupled equations is first proposed for modeling GRNs. In the coupled model, Michaelis-Menten constant associated with regulation by a gene is made invariant irrespective of the gene being regulated. The parameter estimation of the proposed model is carried out using an evolutionary optimization method, namely, trigonometric differential evolution (TDE). Subsequently, the model is further improved and the regulations of different genes by a given gene are made distinct by allowing varying values of Michaelis-Menten constants for each regulation. Apart from making the model more relevant biologically, the improvement results in a decoupled GRN model with fast estimation of model parameters. Further, to enhance exploitation of the search, we propose a local search algorithm based on hill climbing heuristics. A novel mutation operation is also proposed to avoid population stagnation and premature convergence. Real life benchmark data sets generated in vivo are used for validating the proposed model. Further, we also analyze realistic in silico datasets generated using GeneNetweaver. The comparison of the performance of proposed model with other existing methods shows the potential of the proposed model.
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Affiliation(s)
| | - Madhu Chetty
- School of Science, Engineering and Information Technology, Federation University Australia, Gippsland 3842, Australia
| | - Gour Karmakar
- School of Science, Engineering and Information Technology, Federation University Australia, Gippsland 3842, Australia
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35
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Grzegorczyk M, Aderhold A, Husmeier D. Overview and Evaluation of Recent Methods for Statistical Inference of Gene Regulatory Networks from Time Series Data. Methods Mol Biol 2019; 1883:49-94. [PMID: 30547396 DOI: 10.1007/978-1-4939-8882-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
A challenging problem in systems biology is the reconstruction of gene regulatory networks from postgenomic data. A variety of reverse engineering methods from machine learning and computational statistics have been proposed in the literature. However, deciding on the best method to adopt for a particular application or data set might be a confusing task. The present chapter provides a broad overview of state-of-the-art methods with an emphasis on conceptual understanding rather than a deluge of mathematical details, and the pros and cons of the various approaches are discussed. Guidance on practical applications with pointers to publicly available software implementations are included. The chapter concludes with a comprehensive comparative benchmark study on simulated data and a real-work application taken from the current plant systems biology.
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Affiliation(s)
- Marco Grzegorczyk
- Johann Bernoulli Institute, University of Groningen, Groningen, The Netherlands
| | - Andrej Aderhold
- Center for Computer Science, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Dirk Husmeier
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK.
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Castro JC, Valdés I, Gonzalez-García LN, Danies G, Cañas S, Winck FV, Ñústez CE, Restrepo S, Riaño-Pachón DM. Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans. Theor Biol Med Model 2019; 16:7. [PMID: 30961611 PMCID: PMC6454757 DOI: 10.1186/s12976-019-0103-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/07/2019] [Indexed: 11/10/2022] Open
Abstract
Background The increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory networks (GRN). We present a simple yet effective method to estimate transcription factors’ GRNs from transcriptional data. Method We defined interactions between pairs of genes (edges in the GRN) as the partial mutual information between these genes that takes into account time and possible lags in time from one gene in relation to another. We call this method Gene Regulatory Networks on Transfer Entropy (GRNTE) and it corresponds to Granger causality for Gaussian variables in an autoregressive model. To evaluate the reconstruction accuracy of our method, we generated several sub-networks from the GRN of the eukaryotic yeast model, Saccharomyces cerevisae. Then, we applied this method using experimental data of the plant pathogen Phytophthora infestans. We evaluated the transcriptional expression levels of 48 transcription factors of P. infestans during its interaction with one moderately resistant and one susceptible cultivar of yellow potato (Solanum tuberosum group Phureja), using RT-qPCR. With these data, we reconstructed the regulatory network of P. infestans during its interaction with these hosts. Results We first evaluated the performance of our method, based on the transfer entropy (GRNTE), on eukaryotic datasets from the GRNs of the yeast S. cerevisae. Results suggest that GRNTE is comparable with the state-of-the-art methods when the parameters for edge detection are properly tuned. In the case of P. infestans, most of the genes considered in this study, showed a significant change in expression from the onset of the interaction (0 h post inoculum - hpi) to the later time-points post inoculation. Hierarchical clustering of the expression data discriminated two distinct periods during the infection: from 12 to 36 hpi and from 48 to 72 hpi for both the moderately resistant and susceptible cultivars. These distinct periods could be associated with two phases of the life cycle of the pathogen when infecting the host plant: the biotrophic and necrotrophic phases. Conclusions Here we presented an algorithmic solution to the problem of network reconstruction in time series data. This analytical perspective makes use of the dynamic nature of time series data as it relates to intrinsically dynamic processes such as transcription regulation, were multiple elements of the cell (e.g., transcription factors) act simultaneously and change over time. We applied the algorithm to study the regulatory network of P. infestans during its interaction with two hosts which differ in their level of resistance to the pathogen. Although the gene expression analysis did not show differences between the two hosts, the results of the GRN analyses evidenced rewiring of the genes’ interactions according to the resistance level of the host. This suggests that different regulatory processes are activated in response to different environmental cues. Applications of our methodology showed that it could reliably predict where to place edges in the transcriptional networks and sub-networks. The experimental approach used here can help provide insights on the biological role of these interactions on complex processes such as pathogenicity. The code used is available at https://github.com/jccastrog/GRNTE under GNU general public license 3.0. Electronic supplementary material The online version of this article (10.1186/s12976-019-0103-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Camilo Castro
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | - Ivan Valdés
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | | | - Giovanna Danies
- Department of Design, Universidad de los Andes, Bogotá D.C, Colombia
| | - Silvia Cañas
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | - Flavia Vischi Winck
- Regulatory Systems Biology Laboratory, Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carlos Eduardo Ñústez
- School of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá D.C, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C, Colombia
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture, Universidade de São Paulo, Piracicaba, SP, Brazil.
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Maeda K. Gene grouping strategy for network modeling from a small time-series dataset: An illustrative analysis of human organogenesis. Biosystems 2019; 179:24-29. [PMID: 30797967 DOI: 10.1016/j.biosystems.2019.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
Several algorithms have been proposed for modeling a gene regulatory network from a time-series expression dataset, but these have been used in relatively few studies because experimental cost often restricts the number of sampling time points to less than that of genes by more than one order of magnitude. In order to reduce the number of parameters for network modeling, we propose a method for grouping genes by both temporal expression pattern and biological function, modeling interactions between the gene groups by a dynamic Bayesian network approach. Results from applying the method to a gene expression dataset on human organogenesis demonstrate that more biologically plausible results can be obtained by modeling an interaction network for groups of genes than by modeling that for single genes.
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Affiliation(s)
- Kiyohiro Maeda
- Imaging Technology Center, Fujifilm Corporation, 798 Miyanodai, Kaisei-machi, Ashigarakami-gun, Kanagawa, 258-8538, Japan.
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Abstract
Identification of differentially expressed genes has been a high priority task of downstream analyses to further advances in biomedical research. Investigators have been faced with an array of issues in dealing with more complicated experiments and metadata, including batch effects, normalization, temporal dynamics (temporally differential expression), and isoform diversity (isoform-level quantification and differential splicing events). To date, there are currently no standard approaches to precisely and efficiently analyze these moderate or large-scale experimental designs, especially with combined metadata. In this report, we propose comprehensive analytical pipelines to precisely characterize temporal dynamics in differential expression of genes and other genomic features, i.e., the variability of transcripts, isoforms and exons, by controlling batch effects and other nuisance factors that could have significant confounding effects on the main effects of interest in comparative models and may result in misleading interpretations.
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Jana B, Mitra S, Acharyya S. Repository and Mutation based Particle Swarm Optimization (RMPSO): A new PSO variant applied to reconstruction of Gene Regulatory Network. Appl Soft Comput 2019. [DOI: 10.1016/j.asoc.2018.09.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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Raza K. Fuzzy logic based approaches for gene regulatory network inference. Artif Intell Med 2018; 97:189-203. [PMID: 30573378 DOI: 10.1016/j.artmed.2018.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 12/26/2022]
Abstract
The rapid advancements in high-throughput techniques have fueled large-scale production of biological data at very affordable costs. Some of these techniques are microarrays and next-generation sequencing that provide genome level insight of living cells. As a result, the size of most of the biological databases, such as NCBI-GEO, NCBI-SRA, etc., is growing exponentially. These biological data are analyzed using various computational techniques for knowledge discovery - which is also one of the objectives of bioinformatics research. Gene regulatory network (GRN) is a gene-gene interaction network which plays a pivotal role in understanding gene regulation processes and disease mechanism at the molecular level. From last couple of decades, researchers are interested in developing computational algorithms for GRN inference (GRNI) from high-throughput experimental data. Several computational approaches have been proposed for inferring GRN from gene expression data including statistical techniques (correlation coefficient), information theory (mutual information), regression-based approaches, probabilistic approaches (Bayesian networks, naïve byes), artificial neural networks and fuzzy logic. The fuzzy logic, along with its hybridization with other intelligent approaches, is a well-studied technique in GRNI due to its several advantages. In this paper, we present a consolidated review on fuzzy logic and its hybrid approaches developed during last two decades for GRNI.
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Affiliation(s)
- Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India.
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41
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Zhang S, Du Z, Wang JTL, Jiang H. Discovering frequent induced subgraphs from directed networks. INTELL DATA ANAL 2018. [DOI: 10.3233/ida-173681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Sen Zhang
- Department of Mathematics, Computer Science and Statistics, State University of New York (SUNY) College at Oneonta, New York, NY 13820, USA
| | - Zhihui Du
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jason T. L. Wang
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Haodi Jiang
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
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42
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Rubiolo M, Milone DH, Stegmayer G. Extreme learning machines for reverse engineering of gene regulatory networks from expression time series. Bioinformatics 2018; 34:1253-1260. [PMID: 29182723 DOI: 10.1093/bioinformatics/btx730] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 11/21/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation The reconstruction of gene regulatory networks (GRNs) from genes profiles has a growing interest in bioinformatics for understanding the complex regulatory mechanisms in cellular systems. GRNs explicitly represent the cause-effect of regulation among a group of genes and its reconstruction is today a challenging computational problem. Several methods were proposed, but most of them require different input sources to provide an acceptable prediction. Thus, it is a great challenge to reconstruct a GRN only from temporal gene expression data. Results Extreme Learning Machine (ELM) is a new supervised neural model that has gained interest in the last years because of its higher learning rate and better performance than existing supervised models in terms of predictive power. This work proposes a novel approach for GRNs reconstruction in which ELMs are used for modeling the relationships between gene expression time series. Artificial datasets generated with the well-known benchmark tool used in DREAM competitions were used. Real datasets were used for validation of this novel proposal with well-known GRNs underlying the time series. The impact of increasing the size of GRNs was analyzed in detail for the compared methods. The results obtained confirm the superiority of the ELM approach against very recent state-of-the-art methods in the same experimental conditions. Availability and implementation The web demo can be found at http://sinc.unl.edu.ar/web-demo/elm-grnnminer/. The source code is available at https://sourceforge.net/projects/sourcesinc/files/elm-grnnminer. Contact mrubiolo@santafe-conicet.gov.ar. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- M Rubiolo
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, 3000 Santa Fe, Argentina.,Center of Research and Development of Information System Engineering, CIDISI, System Engineering Department, UTN-FRSF, 3000 Santa Fe, Argentina
| | - D H Milone
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, 3000 Santa Fe, Argentina
| | - G Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, 3000 Santa Fe, Argentina
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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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Muthiah A, Angulo MS, Walker NN, Keller SR, Lee JK. Biologically anchored knowledge expansion approach uncovers KLF4 as a novel insulin signaling regulator. PLoS One 2018; 13:e0204100. [PMID: 30240435 PMCID: PMC6150497 DOI: 10.1371/journal.pone.0204100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
One of the biggest challenges in analyzing high throughput omics data in biological studies is extracting information that is relevant to specific biological mechanisms of interest while simultaneously restricting the number of false positive findings. Due to random chances with numerous candidate targets and mechanisms, computational approaches often yield a large number of false positives that cannot easily be discerned from relevant biological findings without costly, and often infeasible, biological experiments. We here introduce and apply an integrative bioinformatics approach, Biologically Anchored Knowledge Expansion (BAKE), which uses sequential statistical analysis and literature mining to identify highly relevant network genes and effectively removes false positive findings. Applying BAKE to genomic expression data collected from mouse (Mus musculus) adipocytes during insulin resistance progression, we uncovered the transcription factor Krueppel-like Factor 4 (KLF4) as a regulator of early insulin signaling. We experimentally confirmed that KLF4 controls the expression of two key insulin signaling molecules, the Insulin Receptor Substrate 2 (IRS2) and Tuberous Sclerosis Complex 2 (TSC2).
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Affiliation(s)
- Annamalai Muthiah
- Department of Systems and Information Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Morgan S. Angulo
- Department of Surgery, University of Virginia Medical Center, University of Virginia, Charlottesville, Virginia, United States of America
| | - Natalie N. Walker
- Department of Medicine, Division of Endocrinology and Metabolism, University of Virginia, Charlottesville, Virginia, United States of America
| | - Susanna R. Keller
- Department of Medicine, Division of Endocrinology and Metabolism, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jae K. Lee
- Department of Systems and Information Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
- Department of Public Health Sciences, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
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Garren JM, Kim J. Bootstrapping Time-Course Gene Expression Data for Gene Networks: Application to Gene Relevance Networks. J Comput Biol 2018; 25:1374-1384. [PMID: 30133320 DOI: 10.1089/cmb.2018.0029] [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: 11/12/2022] Open
Abstract
Identification of gene regulatory networks (GRNs) is a fundamental step to understand the molecular role of each gene and it helps to develop treatment and cure of a disease. To identify GRNs, time-course gene expression data are widely used. However, the identification is hampered by intrinsic attributes of the data such as small sample size, a large number of variables, and complex error structures with high variation. Under this situation, most GRN inference methods utilize point estimators or make numerous assumptions that are often incompatible with the experimental data. Moreover, different inference methods often provide inconsistent results. An alternative to alleviate this problem can be the bootstrap method because it provides more reliable outcomes by integrating results from multiple bootstrap samples without any distributional assumptions. In this study, we propose a bootstrap method for dependent time-course gene expression data and we mainly focus on its application to gene relevance networks. The proposed method is applied to gene networks for zebrafish retina.
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Affiliation(s)
| | - Jaejik Kim
- Department of Statistics, Sungkyunkwan University, Seoul, Korea
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Basili D, Zhang JL, Herbert J, Kroll K, Denslow ND, Martyniuk CJ, Falciani F, Antczak P. In Silico Computational Transcriptomics Reveals Novel Endocrine Disruptors in Largemouth Bass ( Micropterus salmoides). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7553-7565. [PMID: 29878769 DOI: 10.1021/acs.est.8b02805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In recent years, decreases in fish populations have been attributed, in part, to the effect of environmental chemicals on ovarian development. To understand the underlying molecular events we developed a dynamic model of ovary development linking gene transcription to key physiological end points, such as gonadosomatic index (GSI), plasma levels of estradiol (E2) and vitellogenin (VTG), in largemouth bass ( Micropterus salmoides). We were able to identify specific clusters of genes, which are affected at different stages of ovarian development. A subnetwork was identified that closely linked gene expression and physiological end points and by interrogating the Comparative Toxicogenomic Database (CTD), quercetin and tretinoin (ATRA) were identified as two potential candidates that may perturb this system. Predictions were validated by investigation of reproductive associated transcripts using qPCR in ovary and in the liver of both male and female largemouth bass treated after a single injection of quercetin and tretinoin (10 and 100 μg/kg). Both compounds were found to significantly alter the expression of some of these genes. Our findings support the use of omics and online repositories for identification of novel, yet untested, compounds. This is the first study of a dynamic model that links gene expression patterns across stages of ovarian development.
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Affiliation(s)
- Danilo Basili
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
| | - Ji-Liang Zhang
- Henan Open Laboratory of Key Subjects of Environmental and Animal Products Safety, College of Animal Science and Technology , Henan University of Science and Technology , Henan 471003 , China
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - John Herbert
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
| | - Kevin Kroll
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Nancy D Denslow
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine and UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Francesco Falciani
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
| | - Philipp Antczak
- Institute for Integrative Biology, University of Liverpool , L69 7ZB , Liverpool , United Kingdom
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Takenaka Y, Mikami K, Seno S, Matsuda H. Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. BMC Bioinformatics 2018; 19:89. [PMID: 29745848 PMCID: PMC5998889 DOI: 10.1186/s12859-018-2072-y] [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] [Indexed: 11/21/2022] Open
Abstract
Background Comprehensively understanding the dynamics of biological systems is among the biggest current challenges in biology and medicine. To acquire this understanding, researchers have measured the time-series expression profiles of cell lines of various organisms. Biological technologies have also drastically improved, providing a huge amount of information with support from bioinformatics and systems biology. However, the transitions between the activation and inactivation of gene regulations, at the temporal resolution of single time points, are difficult to extract from time-course gene expression profiles. Results Our proposed method reports the activation period of each gene regulation from gene expression profiles and a gene regulatory network. The correctness and effectiveness of the method were validated by analyzing the diauxic shift from glucose to lactose in Escherichia coli. The method completely detected the three periods of the shift; 1) consumption of glucose as nutrient source, 2) the period of seeking another nutrient source and 3) consumption of lactose as nutrient source. We then applied the method to mouse adipocyte differentiation data. Cell differentiation into adipocytes is known to involve two waves of the gene regulation cascade, and sub-waves are predicted. From the gene expression profiles of the cell differentiation process from ES to adipose cells (62 time points), our method acquired four periods; three periods covering the two known waves of the cascade, and a final period of gene regulations when the differentiation to adipocytes was completed. Conclusions Our proposed method identifies the transitions of gene regulations from time-series gene expression profiles. Dynamic analyses are essential for deep understanding of biological systems and for identifying the causes of the onset of diseases such as diabetes and osteoporosis. The proposed method can greatly contribute to the progress of biology and medicine.
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Affiliation(s)
- Yoichi Takenaka
- Faculty of Informatics, Kansai University, Ryousenji 2-1-1, Takatsuki, Osaka, Japan. .,Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan. .,Graduate School of Medicine, Osaka University, Yamadaoka 2, Suita, Osaka, Japan.
| | - Kazuma Mikami
- Recruit Holdings Co. Ltd., Marunouchi 1-9-2, Chiyoda, Tokyo, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan
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Mall R, Cerulo L, Garofano L, Frattini V, Kunji K, Bensmail H, Sabedot TS, Noushmehr H, Lasorella A, Iavarone A, Ceccarelli M. RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes. Nucleic Acids Res 2018; 46:e39. [PMID: 29361062 PMCID: PMC6283452 DOI: 10.1093/nar/gky015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/06/2018] [Indexed: 01/05/2023] Open
Abstract
We propose a generic framework for gene regulatory network (GRN) inference approached as a feature selection problem. GRNs obtained using Machine Learning techniques are often dense, whereas real GRNs are rather sparse. We use a Tikonov regularization inspired optimal L-curve criterion that utilizes the edge weight distribution for a given target gene to determine the optimal set of TFs associated with it. Our proposed framework allows to incorporate a mechanistic active biding network based on cis-regulatory motif analysis. We evaluate our regularization framework in conjunction with two non-linear ML techniques, namely gradient boosting machines (GBM) and random-forests (GENIE), resulting in a regularized feature selection based method specifically called RGBM and RGENIE respectively. RGBM has been used to identify the main transcription factors that are causally involved as master regulators of the gene expression signature activated in the FGFR3-TACC3-positive glioblastoma. Here, we illustrate that RGBM identifies the main regulators of the molecular subtypes of brain tumors. Our analysis reveals the identity and corresponding biological activities of the master regulators characterizing the difference between G-CIMP-high and G-CIMP-low subtypes and between PA-like and LGm6-GBM, thus providing a clue to the yet undetermined nature of the transcriptional events among these subtypes.
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Affiliation(s)
- Raghvendra Mall
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Luigi Cerulo
- Department of Science and Technology, University of Sannio, Benevento, Italy
- BIOGEM Istituto di Ricerche Genetiche “G. Salvatore”, Ariano Irpino, Italy
| | - Luciano Garofano
- Department of Science and Technology, University of Sannio, Benevento, Italy
- BIOGEM Istituto di Ricerche Genetiche “G. Salvatore”, Ariano Irpino, Italy
| | - Veronique Frattini
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA
| | - Khalid Kunji
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Halima Bensmail
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Thais S Sabedot
- Department of Neurosurgery, Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
- Department of Genetics (CISBi/NAP), Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of Sao Paulo, Monte Alegre, Ribeirao Preto, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
- Department of Genetics (CISBi/NAP), Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of Sao Paulo, Monte Alegre, Ribeirao Preto, Brazil
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, New York 10032, USA
| | - Michele Ceccarelli
- Department of Science and Technology, University of Sannio, Benevento, Italy
- BIOGEM Istituto di Ricerche Genetiche “G. Salvatore”, Ariano Irpino, Italy
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Modrák M, Vohradský J. Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data. BMC Bioinformatics 2018; 19:137. [PMID: 29653518 PMCID: PMC5899412 DOI: 10.1186/s12859-018-2138-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/26/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Identifying regulons of sigma factors is a vital subtask of gene network inference. Integrating multiple sources of data is essential for correct identification of regulons and complete gene regulatory networks. Time series of expression data measured with microarrays or RNA-seq combined with static binding experiments (e.g., ChIP-seq) or literature mining may be used for inference of sigma factor regulatory networks. RESULTS We introduce Genexpi: a tool to identify sigma factors by combining candidates obtained from ChIP experiments or literature mining with time-course gene expression data. While Genexpi can be used to infer other types of regulatory interactions, it was designed and validated on real biological data from bacterial regulons. In this paper, we put primary focus on CyGenexpi: a plugin integrating Genexpi with the Cytoscape software for ease of use. As a part of this effort, a plugin for handling time series data in Cytoscape called CyDataseries has been developed and made available. Genexpi is also available as a standalone command line tool and an R package. CONCLUSIONS Genexpi is a useful part of gene network inference toolbox. It provides meaningful information about the composition of regulons and delivers biologically interpretable results.
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Affiliation(s)
- Martin Modrák
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.
| | - Jiří Vohradský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
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50
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Nguyen P, Braun R. Semi-supervised network inference using simulated gene expression dynamics. Bioinformatics 2018; 34:1148-1156. [PMID: 29186340 DOI: 10.1093/bioinformatics/btx748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/23/2017] [Indexed: 01/21/2023] Open
Abstract
Motivation Inferring the structure of gene regulatory networks from high-throughput datasets remains an important and unsolved problem. Current methods are hampered by problems such as noise, low sample size, and incomplete characterizations of regulatory dynamics, leading to networks with missing and anomalous links. Integration of prior network information (e.g. from pathway databases) has the potential to improve reconstructions. Results We developed a semi-supervised network reconstruction algorithm that enables the synthesis of information from partially known networks with time course gene expression data. We adapted partial least square-variable importance in projection (VIP) for time course data and used reference networks to simulate expression data from which null distributions of VIP scores are generated and used to estimate edge probabilities for input expression data. By using simulated dynamics to generate reference distributions, this approach incorporates previously known regulatory relationships and links the network to the dynamics to form a semi-supervised approach that discovers novel and anomalous connections. We applied this approach to data from a sleep deprivation study with KEGG pathways treated as prior networks, as well as to synthetic data from several DREAM challenges, and find that it is able to recover many of the true edges and identify errors in these networks, suggesting its ability to derive posterior networks that accurately reflect gene expression dynamics. Availability and implementation R code is available at https://github.com/pn51/postPLSR. Contact rbraun@northwestern.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Phan Nguyen
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
| | - Rosemary Braun
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA.,Biostatistics Division, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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