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Chang JR, Yao ZF, Hsieh S, Nordling TEM. Age Prediction Using Resting-State Functional MRI. Neuroinformatics 2024; 22:119-134. [PMID: 38341830 DOI: 10.1007/s12021-024-09653-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2023] [Indexed: 02/13/2024]
Abstract
The increasing lifespan and large individual differences in cognitive capability highlight the importance of comprehending the aging process of the brain. Contrary to visible signs of bodily ageing, like greying of hair and loss of muscle mass, the internal changes that occur within our brains remain less apparent until they impair function. Brain age, distinct from chronological age, reflects our brain's health status and may deviate from our actual chronological age. Notably, brain age has been associated with mortality and depression. The brain is plastic and can compensate even for severe structural damage by rewiring. Functional characterization offers insights that structural cannot provide. Contrary to the multitude of studies relying on structural magnetic resonance imaging (MRI), we utilize resting-state functional MRI (rsfMRI). We also address the issue of inclusion of subjects with abnormal brain ageing through outlier removal. In this study, we employ the Least Absolute Shrinkage and Selection Operator (LASSO) to identify the 39 most predictive correlations derived from the rsfMRI data. The data is from a cohort of 176 healthy right-handed volunteers, aged 18-78 years (95/81 male/female, mean age 48, SD 17) collected at the Mind Research Imaging Center at the National Cheng Kung University. We establish a normal reference model by excluding 68 outliers, which achieves a leave-one-out mean absolute error of 2.48 years. By asking which additional features that are needed to predict the chronological age of the outliers with a smaller error, we identify correlations predictive of abnormal aging. These are associated with the Default Mode Network (DMN). Our normal reference model has the lowest prediction error among published models evaluated on adult subjects of almost all ages and is thus a candidate for screening for abnormal brain aging that has not yet manifested in cognitive decline. This study advances our ability to predict brain aging and provides insights into potential biomarkers for assessing brain age, suggesting that the role of DMN in brain aging should be studied further.
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Affiliation(s)
- Jose Ramon Chang
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan
| | - Zai-Fu Yao
- College of Education, National Tsing Hua University, Hsinchu, 30013, Taiwan
- Research Center for Education and Mind Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan
- Department of Kinesiology, National Tsing Hua University, Hsinchu, 30013, Taiwan
- Basic Psychology Group, Department of Educational Psychology and Counseling, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shulan Hsieh
- Department of Psychology, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan
- Institute of Allied Health Sciences, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan
- Department of Public Health, College of Medicine, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan.
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Wu YH, Nordling TEM. Taiwan ended third COVID-19 community outbreak as forecasted. Sci Rep 2024; 14:6596. [PMID: 38503791 PMCID: PMC10951404 DOI: 10.1038/s41598-024-56692-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/09/2024] [Indexed: 03/21/2024] Open
Abstract
Accurate forecasting of community outbreaks is crucial for governments to allocate healthcare resources correctly and implement suitable non-pharmaceutical interventions. Additionally, companies must address critical questions about stock and staff management. Society's key concern is when businesses and organizations can resume normal operations. Between December 31st 2019 and 2021, Taiwan experienced three separate COVID-19 community outbreaks with significant time intervals in between, suggesting that each outbreak eventually came to an end. We identified the ratio of the 7-day average of local & unknown confirmed to suspected cases as the key control variable and forecasted the end of the third outbreak by the exponential model. We forecasted the end of the third outbreak on Aug. 16th with threshold ratios of 1.2 · 10 - 4 . The real observations crossed the threshold on Aug. 27th, eleven days later than forecasted, with the last case of the third outbreak confirmed and quarantined on Sept. 20th. This demonstrated the accuracy of the proposed forecasting method in predicting the end of a local outbreak. Furthermore, we highlight that the ratio reflects the effectiveness of contact tracing. Effective contact tracing together with testing and isolation of infected individuals is crucial for ending community outbreaks.
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Affiliation(s)
- Yu-Heng Wu
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, 701, Taiwan.
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Ashyani A, Wu YH, Hsu HW, Nordling TEM. Ideal adaptive control in biological systems: an analysis of P -invariance and dynamical compensation properties. BMC Bioinformatics 2024; 25:95. [PMID: 38438950 PMCID: PMC10913207 DOI: 10.1186/s12859-024-05718-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Dynamical compensation (DC) provides robustness to parameter fluctuations. As an example, DC enables control of the functional mass of endocrine or neuronal tissue essential for controlling blood glucose by insulin through a nonlinear feedback loop. Researchers have shown that DC is related to the structural unidentifiability and the P -invariance property. The P -invariance property is a sufficient and necessary condition for the DC property. DC has been seen in systems with at least three dimensions. In this article, we discuss DC and P -invariance from an adaptive control perspective. An adaptive controller automatically adjusts its parameters to optimise performance, maintain stability, and deal with uncertainties in a system. RESULTS We initiate our analysis by introducing a simplified two-dimensional dynamical model with DC, fostering experimentation and understanding of the system's behavior. We explore the system's behavior with time-varying input and disturbance signals, with a focus on illustrating the system's P -invariance properties in phase portraits and step-like response graphs. CONCLUSIONS We show that DC can be seen as a case of ideal adaptive control since the system is invariant to the compensated parameter.
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Affiliation(s)
- Akram Ashyani
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan
| | - Yu-Heng Wu
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan
| | - Huan-Wei Hsu
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan, 701, Taiwan.
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Huang HL, Weng CH, Nordling TEM, Liou YF. Thermalprogan: A sequence-based thermally stable protein generator trained using unpaired data. J Bioinform Comput Biol 2023; 21:2350008. [PMID: 36999645 DOI: 10.1142/s0219720023500087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
MOTIVATION The synthesis of proteins with novel desired properties is challenging but sought after by the industry and academia. The dominating approach is based on trial-and-error inducing point mutations, assisted by structural information or predictive models built with paired data that are difficult to collect. This study proposes a sequence-based unpaired-sample of novel protein inventor (SUNI) to build ThermalProGAN for generating thermally stable proteins based on sequence information. RESULTS The ThermalProGAN can strongly mutate the input sequence with a median number of 32 residues. A known normal protein, 1RG0, was used to generate a thermally stable form by mutating 51 residues. After superimposing the two structures, high similarity is shown, indicating that the basic function would be conserved. Eighty four molecular dynamics simulation results of 1RG0 and the COVID-19 vaccine candidates with a total simulation time of 840[Formula: see text]ns indicate that the thermal stability increased. CONCLUSION This proof of concept demonstrated that transfer of a desired protein property from one set of proteins is feasible. Availability and implementation: The source code of ThermalProGAN can be freely accessed at https://github.com/markliou/ThermalProGAN/ with an MIT license. The website is https://thermalprogan.markliou.tw:433. Supplementary information: Supplementary data are available on Github.
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Affiliation(s)
- Hui-Ling Huang
- International Program of Health Informatics and Management, College of Management, Chang Gung University, No. 259, Wenhua 1st Road Guishan District, Taoyuan City 33302, Taiwan
| | - Chong-Heng Weng
- Department of Computer Science and Information Engineering, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan City 320317, Taiwan
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City 701, Taiwan
- Department of Applied Physics and Electronics, Umeå University 90187 Umeå, Sweden
| | - Yi-Fan Liou
- Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City 701, Taiwan
- Department of Virtual-Reality Interaction with Artificial Intelligence Technology, Coretronic Reality Incorporation, No. 5, Wenhua Rd., Hukou Township, Hsinchu County 303, Taiwan
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Seçilmiş D, Hillerton T, Morgan D, Tjärnberg A, Nelander S, Nordling TEM, Sonnhammer ELL. Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data. NPJ Syst Biol Appl 2020; 6:37. [PMID: 33168813 PMCID: PMC7652823 DOI: 10.1038/s41540-020-00154-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
The interactions among the components of a living cell that constitute the gene regulatory network (GRN) can be inferred from perturbation-based gene expression data. Such networks are useful for providing mechanistic insights of a biological system. In order to explore the feasibility and quality of GRN inference at a large scale, we used the L1000 data where ~1000 genes have been perturbed and their expression levels have been quantified in 9 cancer cell lines. We found that these datasets have a very low signal-to-noise ratio (SNR) level causing them to be too uninformative to infer accurate GRNs. We developed a gene reduction pipeline in which we eliminate uninformative genes from the system using a selection criterion based on SNR, until reaching an informative subset. The results show that our pipeline can identify an informative subset in an overall uninformative dataset, allowing inference of accurate subset GRNs. The accurate GRNs were functionally characterized and potential novel cancer-related regulatory interactions were identified.
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Affiliation(s)
- Deniz Seçilmiş
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Thomas Hillerton
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Daniel Morgan
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Andreas Tjärnberg
- Center for Developmental Genetics, New York University, New York, NY, USA
| | - Sven Nelander
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden.
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Hsia FC, Tang DM, Jevasuwan W, Fukata N, Zhou X, Mitome M, Bando Y, Nordling TEM, Golberg D. Realization and direct observation of five normal and parametric modes in silicon nanowire resonators by in situ transmission electron microscopy. Nanoscale Adv 2019; 1:1784-1790. [PMID: 36134225 PMCID: PMC9418527 DOI: 10.1039/c8na00373d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 02/24/2019] [Indexed: 05/13/2023]
Abstract
Mechanical resonators have wide applications in sensing bio-chemical substances, and provide an accurate method to measure the intrinsic elastic properties of oscillating materials. A high resonance order with high response frequency and a small resonator mass are critical for enhancing the sensitivity and precision. Here, we report on the realization and direct observation of high-order and high-frequency silicon nanowire (Si NW) resonators. By using an oscillating electric-field for inducing a mechanical resonance of single-crystalline Si NWs inside a transmission electron microscope (TEM), we observed resonance up to the 5th order, for both normal and parametric modes at ∼100 MHz frequencies. The precision of the resonant frequency was enhanced, as the deviation reduced from 3.14% at the 1st order to 0.25% at the 5th order, correlating with the increase of energy dissipation. The elastic modulus of Si NWs was measured to be ∼169 GPa in the [110] direction, and size scaling effects were found to be absent down to the ∼20 nm level.
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Affiliation(s)
- Feng-Chun Hsia
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
- Department of Mechanical Engineering, National Cheng Kung University No. 1, University Road Tainan City 701 Taiwan
- Advanced Research Center for Nanolithography (ARCNL) Science Park 106 Amsterdam 1098 XG The Netherlands
| | - Dai-Ming Tang
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
| | - Wipakorn Jevasuwan
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
| | - Naoki Fukata
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
| | - Xin Zhou
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
| | - Masanori Mitome
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
| | - Yoshio Bando
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
- Australian Institute for Innovative Materials, University of Wollongong Wollongong New South Wales 2500 Australia
- Institute of Molecular Plus, Tianjin University No. 11 Building, No. 92 Weijin Road, Nankai District Tianjin 300072 P. R. China
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University No. 1, University Road Tainan City 701 Taiwan
| | - Dmitri Golberg
- International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology (QUT) 2nd George Str. Brisbane QLD 4000 Australia
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Wu WS, Jiang YX, Chang JW, Chu YH, Chiu YH, Tsao YH, Nordling TEM, Tseng YY, Tseng JT. HRPDviewer: human ribosome profiling data viewer. Database (Oxford) 2018; 2018:5052387. [PMID: 30010738 PMCID: PMC6041748 DOI: 10.1093/database/bay074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/19/2018] [Indexed: 12/04/2022]
Abstract
Translational regulation plays an important role in protein synthesis. Dysregulation of translation causes abnormal cell physiology and leads to diseases such as inflammatory disorders and cancers. An emerging technique, called ribosome profiling (ribo-seq), was developed to capture a snapshot of translation. It is based on deep sequencing of ribosome-protected mRNA fragments. A lot of ribo-seq data have been generated in various studies, so databases are needed for depositing and visualizing the published ribo-seq data. Nowadays, GWIPS-viz, RPFdb and TranslatomeDB are the three largest databases developed for this purpose. However, two challenges remain to be addressed. First, GWIPS-viz and RPFdb databases align the published ribo-seq data to the genome. Since ribo-seq data aim to reveal the actively translated mRNA transcripts, there are advantages of aligning ribo-req data to the transcriptome over the genome. Second, TranslatomeDB does not provide any visualization and the other two databases only provide visualization of the ribo-seq data around a specific genomic location, while simultaneous visualization of the ribo-seq data on multiple mRNA transcripts produced from the same gene or different genes is desired. To address these two challenges, we developed the Human Ribosome Profiling Data viewer (HRPDviewer). HRPDviewer (i) contains 610 published human ribo-seq datasets from Gene Expression Omnibus, (ii) aligns the ribo-seq data to the transcriptome and (iii) provides visualization of the ribo-seq data on the selected mRNA transcripts. Using HRPDviewer, researchers can compare the ribosome binding patterns of multiple mRNA transcripts from the same gene or different genes to gain an accurate understanding of protein synthesis in human cells. We believe that HRPDviewer is a useful resource for researchers to study translational regulation in human. Database URL: http://cosbi4.ee.ncku.edu.tw/HRPDviewer/ or http://cosbi5.ee.ncku.edu.tw/HRPDviewer/
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Affiliation(s)
- Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
| | - Yu-Xuan Jiang
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
| | - Jer-Wei Chang
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
| | - Yu-Han Chu
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
| | - Yi-Hao Chiu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
| | - Yi-Hong Tsao
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Joseph T Tseng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No.1, University Road, Tainan City, Taiwan
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Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Nat Commun 2018; 9:4418. [PMID: 30356117 PMCID: PMC6200745 DOI: 10.1038/s41467-018-06735-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/12/2018] [Indexed: 01/17/2023] Open
Abstract
The response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine whether pre- or early post-exposure molecular factors could predict physiologic responses to viral exposure. Using peripheral blood gene expression profiles collected from healthy subjects prior to exposure to one of four respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV), as well as up to 24 h following exposure, we find that it is possible to construct models predictive of symptomatic response using profiles even prior to viral exposure. Analysis of predictive gene features reveal little overlap among models; however, in aggregate, these genes are enriched for common pathways. Heme metabolism, the most significantly enriched pathway, is associated with a higher risk of developing symptoms following viral exposure. This study demonstrates that pre-exposure molecular predictors can be identified and improves our understanding of the mechanisms of response to respiratory viruses.
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Affiliation(s)
- Slim Fourati
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Aarthi Talla
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mehrad Mahmoudian
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
- Department of Future Technologies, University of Turku, FI-20014 Turku, Finland
| | - Joshua G Burkhart
- Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
- Laboratory of Evolutionary Genetics, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Riku Klén
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Thomas Yu
- Sage Bionetworks, Seattle, WA, 98121, USA
| | - Zafer Aydın
- Department of Computer Engineering, Abdullah Gul University, Kayseri, 38080, Turkey
| | - Ka Yee Yeung
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, WA, 98402, USA
| | - Mehmet Eren Ahsen
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Reem Almugbel
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, WA, 98402, USA
| | | | - Xiao Liang
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, WA, 98402, USA
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Motoki Shiga
- Department of Electrical, Electronic and Computer Engineering, Faculty of Engineering, Gifu University, Gifu, 501-1193, Japan
| | - Ana Stanescu
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Computer Science, University of West Georgia, Carrolton, GA, 30116, USA
| | - Robert Vogel
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- IBM T.J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Medical Service, Durham VA Health Care System, Durham, NC, 27705, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Christopher W Woods
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Medical Service, Durham VA Health Care System, Durham, NC, 27705, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Laura L Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Ephraim L Tsalik
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Emergency Medicine Service, Durham VA Health Care System, Durham, NC, 27705, USA
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Morgan D, Tjärnberg A, Nordling TEM, Sonnhammer ELL. A generalized framework for controlling FDR in gene regulatory network inference. Bioinformatics 2018; 35:1026-1032. [DOI: 10.1093/bioinformatics/bty764] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/23/2018] [Accepted: 08/28/2018] [Indexed: 12/23/2022] Open
Affiliation(s)
- Daniel Morgan
- Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Andreas Tjärnberg
- Department of Physics, Chemistry and Biology/Bioinformatics, Linköping University, Linköping, Sweden
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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10
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Celano U, Hsia FC, Vanhaeren D, Paredis K, Nordling TEM, Buijnsters JG, Hantschel T, Vandervorst W. Mesoscopic physical removal of material using sliding nano-diamond contacts. Sci Rep 2018; 8:2994. [PMID: 29445103 PMCID: PMC5813091 DOI: 10.1038/s41598-018-21171-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/31/2018] [Indexed: 11/13/2022] Open
Abstract
Wear mechanisms including fracture and plastic deformation at the nanoscale are central to understand sliding contacts. Recently, the combination of tip-induced material erosion with the sensing capability of secondary imaging modes of AFM, has enabled a slice-and-view tomographic technique named AFM tomography or Scalpel SPM. However, the elusive laws governing nanoscale wear and the large quantity of atoms involved in the tip-sample contact, require a dedicated mesoscale description to understand and model the tip-induced material removal. Here, we study nanosized sliding contacts made of diamond in the regime whereby thousands of nm3 are removed. We explore the fundamentals of high-pressure tip-induced material removal for various materials. Changes in the load force are systematically combined with AFM and SEM to increase the understanding and the process controllability. The nonlinear variation of the removal rate with the load force is interpreted as a combination of two contact regimes each dominating in a particular force range. By using the gradual transition between the two regimes, (1) the experimental rate of material eroded on each tip passage is modeled, (2) a controllable removal rate below 5 nm/scan for all the materials is demonstrated, thus opening to future development of 3D tomographic AFM.
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Affiliation(s)
| | - Feng-Chun Hsia
- IMEC, Kapeldreef 75, B-3001, Heverlee, Belgium.,Department of Mechanical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | | | | | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Josephus G Buijnsters
- Department of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628 CD, Delft, The Netherlands
| | | | - Wilfried Vandervorst
- IMEC, Kapeldreef 75, B-3001, Heverlee, Belgium.,Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001, Leuven, Belgium
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Wu WS, Tu HP, Chu YH, Nordling TEM, Tseng YY, Liaw HJ. YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. Database (Oxford) 2018; 2018:5145122. [PMID: 30371756 PMCID: PMC6204766 DOI: 10.1093/database/bay116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/29/2018] [Indexed: 12/18/2022]
Abstract
Post-translational modifications of histones (e.g. acetylation, methylation, phosphorylation and ubiquitination) play crucial roles in regulating gene expression by altering chromatin structures and creating docking sites for histone/chromatin regulators. However, the combination patterns of histone modifications, regulatory proteins and their corresponding target genes remain incompletely understood. Therefore, it is advantageous to have a tool for the enrichment/depletion analysis of histone modifications and histone/chromatin regulators from a gene list. Many ChIP-chip/ChIP-seq datasets of histone modifications and histone/chromatin regulators in yeast can be found in the literature. Knowing the needs and having the data motivate us to develop a web tool, called Yeast Histone Modifications Identifier (YHMI), which can identify the enriched/depleted histone modifications and the enriched histone/chromatin regulators from a list of yeast genes. Both tables and figures are provided to visualize the identification results. Finally, the high-quality and biological insight of the identification results are demonstrated by two case studies. We believe that YHMI is a valuable tool for yeast biologists to do epigenetics research.
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Affiliation(s)
- Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Ping Tu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Han Chu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI, USA
| | - Hung-Jiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
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Magnusson R, Mariotti GP, Köpsén M, Lövfors W, Gawel DR, Jörnsten R, Linde J, Nordling TEM, Nyman E, Schulze S, Nestor CE, Zhang H, Cedersund G, Benson M, Tjärnberg A, Gustafsson M. LASSIM-A network inference toolbox for genome-wide mechanistic modeling. PLoS Comput Biol 2017. [PMID: 28640810 PMCID: PMC5501685 DOI: 10.1371/journal.pcbi.1005608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM works in two steps, where it first infers a non-linear ODE system of the pre-specified core gene expression. Second, LASSIM in parallel optimizes the parameters that model the regulation of peripheral genes by core system genes. We showed the usefulness of this method by applying LASSIM to infer a large-scale non-linear model of naïve Th2 cell differentiation, made possible by integrating Th2 specific bindings, time-series together with six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models with truly systems-level data. We demonstrate the power of this approach by inferring a mechanistically motivated, genome-wide model of the Th2 transcription regulatory system, which plays an important role in several immune related diseases. There are excellent methods to mathematically model time-resolved biological data on a small scale using accurate mechanistic models. Despite the rapidly increasing availability of such data, mechanistic models have not been applied on a genome-wide level due to excessive runtimes and the non-identifiability of model parameters. However, genome-wide, mechanistic models could potentially answer key clinical questions, such as finding the best drug combinations to induce an expression change from a disease to a healthy state. We present LASSIM, which is a toolbox built to infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the network inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces computation time.
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Affiliation(s)
- Rasmus Magnusson
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Guido Pio Mariotti
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Mattias Köpsén
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - William Lövfors
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Danuta R. Gawel
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Rebecka Jörnsten
- Mathematical Sciences, Chalmers University of Technology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Linde
- Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Research Group Systems Biology and Bioinformatics, Jena, Germany
- Research Group PiDOMICS, Leibniz Institute for Natural Product Research and Infection Biology -Hans Knöll Institute, Jena, Germany
| | - Torbjörn E. M. Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
- Stockholm Bioinformatics Center, Science for Life Laboratory, Solna, Sweden
| | - Elin Nyman
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Sylvie Schulze
- Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Research Group Systems Biology and Bioinformatics, Jena, Germany
| | - Colm E. Nestor
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Huan Zhang
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Gunnar Cedersund
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
- Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Mikael Benson
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Andreas Tjärnberg
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
- * E-mail:
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Tjärnberg A, Morgan DC, Studham M, Nordling TEM, Sonnhammer ELL. GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties. Mol BioSyst 2017; 13:1304-1312. [DOI: 10.1039/c7mb00058h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method.
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Affiliation(s)
- Andreas Tjärnberg
- Stockholm Bioinformatics Center
- Science for Life Laboratory
- Sweden
- Department of Biochemistry and Biophysics
- Stockholm University
| | - Daniel C. Morgan
- Stockholm Bioinformatics Center
- Science for Life Laboratory
- Sweden
- Department of Biochemistry and Biophysics
- Stockholm University
| | - Matthew Studham
- Stockholm Bioinformatics Center
- Science for Life Laboratory
- Sweden
- Department of Biochemistry and Biophysics
- Stockholm University
| | - Torbjörn E. M. Nordling
- Stockholm Bioinformatics Center
- Science for Life Laboratory
- Sweden
- Department of Mechanical Engineering
- National Cheng Kung University
| | - Erik L. L. Sonnhammer
- Stockholm Bioinformatics Center
- Science for Life Laboratory
- Sweden
- Department of Biochemistry and Biophysics
- Stockholm University
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14
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Padhan N, Nordling TEM, Sundström M, Åkerud P, Birgisson H, Nygren P, Nelander S, Claesson-Welsh L. High sensitivity isoelectric focusing to establish a signaling biomarker for the diagnosis of human colorectal cancer. BMC Cancer 2016; 16:683. [PMID: 27562229 PMCID: PMC5000422 DOI: 10.1186/s12885-016-2725-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 08/15/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The progression of colorectal cancer (CRC) involves recurrent amplifications/mutations in the epidermal growth factor receptor (EGFR) and downstream signal transducers of the Ras pathway, KRAS and BRAF. Whether genetic events predicted to result in increased and constitutive signaling indeed lead to enhanced biological activity is often unclear and, due to technical challenges, unexplored. Here, we investigated proliferative signaling in CRC using a highly sensitive method for protein detection. The aim of the study was to determine whether multiple changes in proliferative signaling in CRC could be combined and exploited as a "complex biomarker" for diagnostic purposes. METHODS We used robotized capillary isoelectric focusing as well as conventional immunoblotting for the comprehensive analysis of epidermal growth factor receptor signaling pathways converging on extracellular regulated kinase 1/2 (ERK1/2), AKT, phospholipase Cγ1 (PLCγ1) and c-SRC in normal mucosa compared with CRC stage II and IV. Computational analyses were used to test different activity patterns for the analyzed signal transducers. RESULTS Signaling pathways implicated in cell proliferation were differently dysregulated in CRC and, unexpectedly, several were downregulated in disease. Thus, levels of activated ERK1 (pERK1), but not pERK2, decreased in stage II and IV while total ERK1/2 expression remained unaffected. In addition, c-SRC expression was lower in CRC compared with normal tissues and phosphorylation on the activating residue Y418 was not detected. In contrast, PLCγ1 and AKT expression levels were elevated in disease. Immunoblotting of the different signal transducers, run in parallel to capillary isoelectric focusing, showed higher variability and lower sensitivity and resolution. Computational analyses showed that, while individual signaling changes lacked predictive power, using the combination of changes in three signaling components to create a "complex biomarker" allowed with very high accuracy, the correct diagnosis of tissues as either normal or cancerous. CONCLUSIONS We present techniques that allow rapid and sensitive determination of cancer signaling that can be used to differentiate colorectal cancer from normal tissue.
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Affiliation(s)
- Narendra Padhan
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv 20, Uppsala, 751 85, Sweden
| | - Torbjörn E M Nordling
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv 20, Uppsala, 751 85, Sweden.,Stockholm Bioinformatics Centre, Science for Life Laboratory, Box 1031, 171 21, Solna, Sweden.,Current address: Department of Mechanical Engineering, National Cheng Kung University, No. 1 University Road, Tainan, 70101, Taiwan
| | - Magnus Sundström
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv 20, Uppsala, 751 85, Sweden
| | - Peter Åkerud
- Department Surgical Sciences, Uppsala University, 751 85, Uppsala, Sweden
| | - Helgi Birgisson
- Department Surgical Sciences, Uppsala University, 751 85, Uppsala, Sweden
| | - Peter Nygren
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv 20, Uppsala, 751 85, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv 20, Uppsala, 751 85, Sweden
| | - Lena Claesson-Welsh
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv 20, Uppsala, 751 85, Sweden.
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15
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Tjärnberg A, Nordling TEM, Studham M, Nelander S, Sonnhammer ELL. Avoiding pitfalls in L1-regularised inference of gene networks. Mol BioSyst 2015; 11:287-96. [DOI: 10.1039/c4mb00419a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
L1 regularisation methods fail to infer the correct network even when the data are so informative that all existing links can be proven to exist.
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Affiliation(s)
- Andreas Tjärnberg
- Stockholm Bioinformatics Centre
- Science for Life Laboratory
- 17121 Solna
- Sweden
- Department of Biochemistry and Biophysics
| | - Torbjörn E. M. Nordling
- Stockholm Bioinformatics Centre
- Science for Life Laboratory
- 17121 Solna
- Sweden
- Department of Immunology
| | - Matthew Studham
- Stockholm Bioinformatics Centre
- Science for Life Laboratory
- 17121 Solna
- Sweden
| | - Sven Nelander
- Department of Immunology
- Genetics and Pathology
- Uppsala University
- Rudbeck laboratory
- 75185 Uppsala
| | - Erik L. L. Sonnhammer
- Stockholm Bioinformatics Centre
- Science for Life Laboratory
- 17121 Solna
- Sweden
- Department of Biochemistry and Biophysics
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16
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Studham ME, Tjärnberg A, Nordling TEM, Nelander S, Sonnhammer ELL. Functional association networks as priors for gene regulatory network inference. ACTA ACUST UNITED AC 2014; 30:i130-8. [PMID: 24931976 PMCID: PMC4058914 DOI: 10.1093/bioinformatics/btu285] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Motivation: Gene regulatory network (GRN) inference reveals the influences genes have on one another in cellular regulatory systems. If the experimental data are inadequate for reliable inference of the network, informative priors have been shown to improve the accuracy of inferences. Results: This study explores the potential of undirected, confidence-weighted networks, such as those in functional association databases, as a prior source for GRN inference. Such networks often erroneously indicate symmetric interaction between genes and may contain mostly correlation-based interaction information. Despite these drawbacks, our testing on synthetic datasets indicates that even noisy priors reflect some causal information that can improve GRN inference accuracy. Our analysis on yeast data indicates that using the functional association databases FunCoup and STRING as priors can give a small improvement in GRN inference accuracy with biological data. Contact:matthew.studham@scilifelab.se Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew E Studham
- Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, SwedenStockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, Sweden
| | - Andreas Tjärnberg
- Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, SwedenStockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, Sweden
| | - Torbjörn E M Nordling
- Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, SwedenStockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, Sweden
| | - Sven Nelander
- Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, Sweden
| | - Erik L L Sonnhammer
- Stockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, SwedenStockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, SwedenStockholm Bioinformatics Centre, Science for Life Laboratory, SE-171 65 Solna, Sweden, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden and Swedish eScience Research Center, SE-100 44 Stockholm, Sweden
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17
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Jörnsten R, Abenius T, Kling T, Schmidt L, Johansson E, Nordling TEM, Nordlander B, Sander C, Gennemark P, Funa K, Nilsson B, Lindahl L, Nelander S. Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol Syst Biol 2011; 7:486. [PMID: 21525872 PMCID: PMC3101951 DOI: 10.1038/msb.2011.17] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 03/21/2011] [Indexed: 12/25/2022] Open
Abstract
DNA copy number aberrations (CNAs) are a hallmark of cancer genomes. However, little is known about how such changes affect global gene expression. We develop a modeling framework, EPoC (Endogenous Perturbation analysis of Cancer), to (1) detect disease-driving CNAs and their effect on target mRNA expression, and to (2) stratify cancer patients into long- and short-term survivors. Our method constructs causal network models of gene expression by combining genome-wide DNA- and RNA-level data. Prognostic scores are obtained from a singular value decomposition of the networks. By applying EPoC to glioblastoma data from The Cancer Genome Atlas consortium, we demonstrate that the resulting network models contain known disease-relevant hub genes, reveal interesting candidate hubs, and uncover predictors of patient survival. Targeted validations in four glioblastoma cell lines support selected predictions, and implicate the p53-interacting protein Necdin in suppressing glioblastoma cell growth. We conclude that large-scale network modeling of the effects of CNAs on gene expression may provide insights into the biology of human cancer. Free software in MATLAB and R is provided.
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Affiliation(s)
- Rebecka Jörnsten
- Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden
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Nordling TEM, Hiroi N, Funahashi A, Kitano H. Deduction of intracellular sub-systems from a topological description of the network. Mol BioSyst 2007; 3:523-9. [PMID: 17639126 DOI: 10.1039/b702142a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-linear behaviour of biochemical networks, such as intracellular gene, protein or metabolic networks, is commonly represented using graphs of the underlying topology. Nodes represent abundance of molecules and edges interactions between pairs of molecules. These graphs are linear and thus based on an implicit linearization of the kinetic reactions in one or several dynamic modes of the total system. It is common to use data from different sources -- experiments conducted under different conditions or even on different species -- meaning that the graph will be a superposition of linearizations made in many different modes. The mixing of different modes makes it hard to identify functional modules, that is sub-systems that carry out a specific biological function, since the graph will contain many interactions that do not naturally occur at the same time. The ability to establish a boundary between the sub-system and its environment is critical in the definition of a module, contrary to a motif in which only internal interactions count. Identification of functional modules should therefore be done on graphs depicting the mode in which their function is carried out, i.e. graphs that only contain edges representing interactions active in the specific mode. In general, when an interaction between two molecules is established, one should always state the mode of the system in which it is active.
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Affiliation(s)
- Torbjörn E M Nordling
- Automatic Control - School of Electrical Engineering, Royal Institute of Technology (KTH), Sweden.
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