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Dear R, Wagstyl K, Seidlitz J, Markello RD, Arnatkevičiūtė A, Anderson KM, Bethlehem RAI, Raznahan A, Bullmore ET, Vértes PE. Cortical gene expression architecture links healthy neurodevelopment to the imaging, transcriptomics and genetics of autism and schizophrenia. Nat Neurosci 2024; 27:1075-1086. [PMID: 38649755 PMCID: PMC11156586 DOI: 10.1038/s41593-024-01624-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
Human brain organization involves the coordinated expression of thousands of genes. For example, the first principal component (C1) of cortical transcription identifies a hierarchy from sensorimotor to association regions. In this study, optimized processing of the Allen Human Brain Atlas revealed two new components of cortical gene expression architecture, C2 and C3, which are distinctively enriched for neuronal, metabolic and immune processes, specific cell types and cytoarchitectonics, and genetic variants associated with intelligence. Using additional datasets (PsychENCODE, Allen Cell Atlas and BrainSpan), we found that C1-C3 represent generalizable transcriptional programs that are coordinated within cells and differentially phased during fetal and postnatal development. Autism spectrum disorder and schizophrenia were specifically associated with C1/C2 and C3, respectively, across neuroimaging, differential expression and genome-wide association studies. Evidence converged especially in support of C3 as a normative transcriptional program for adolescent brain development, which can lead to atypical supragranular cortical connectivity in people at high genetic risk for schizophrenia.
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Affiliation(s)
- Richard Dear
- Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | | | - Jakob Seidlitz
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross D Markello
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Aurina Arnatkevičiūtė
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | | | | | - Armin Raznahan
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA
| | | | - Petra E Vértes
- Department of Psychiatry, University of Cambridge, Cambridge, UK
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2
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Castaneda EU, Baker EJ. KNeXT: a NetworkX-based topologically relevant KEGG parser. Front Genet 2024; 15:1292394. [PMID: 38415058 PMCID: PMC10896898 DOI: 10.3389/fgene.2024.1292394] [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: 09/12/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
Automating the recreation of gene and mixed gene-compound networks from Kyoto Encyclopedia of Genes and Genomes (KEGG) Markup Language (KGML) files is challenging because the data structure does not preserve the independent or loosely connected neighborhoods in which they were originally derived, referred to here as its topological environment. Identical accession numbers may overlap, causing neighborhoods to artificially collapse based on duplicated identifiers. This causes current parsers to create misleading or erroneous graphical representations when mixed gene networks are converted to gene-only networks. To overcome these challenges we created a python-based KEGG NetworkX Topological (KNeXT) parser that allows users to accurately recapitulate genetic networks and mixed networks from KGML map data. The software, archived as a python package index (PyPI) file to ensure broad application, is designed to ingest KGML files through built-in APIs and dynamically create high-fidelity topological representations. The utilization of NetworkX's framework to generate tab-separated files additionally ensures that KNeXT results may be imported into other graph frameworks and maintain programmatic access to the original x-y axis positions to each node in the KEGG pathway. KNeXT is a well-described Python 3 package that allows users to rapidly download and aggregate specific KGML files and recreate KEGG pathways based on a range of user-defined settings. KNeXT is platform-independent, distinctive, and it is not written on top of other Python parsers. Furthermore, KNeXT enables users to parse entire local folders or single files through command line scripts and convert the output into NCBI or UniProt IDs. KNeXT provides an ability for researchers to generate pathway visualizations while persevering the original context of a KEGG pathway. Source code is freely available at https://github.com/everest-castaneda/knext.
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Affiliation(s)
- Everest Uriel Castaneda
- Department of Biology, Baylor University, Waco, TX, United States
- School of Engineering and Computer Science, Baylor University, Waco, TX, United States
| | - Erich J Baker
- Department of Mathematics and Computer Science, Belmont University, Nashville, TN, United States
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3
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Pannala VR, Wallqvist A. High-Throughput Transcriptomics Differentiates Toxic versus Non-Toxic Chemical Exposures Using a Rat Liver Model. Int J Mol Sci 2023; 24:17425. [PMID: 38139254 PMCID: PMC10743995 DOI: 10.3390/ijms242417425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
To address the challenge of limited throughput with traditional toxicity testing, a newly developed high-throughput transcriptomics (HTT) platform, together with a 5-day in vivo rat model, offers an alternative approach to estimate chemical exposures and provide reasonable estimates of toxicological endpoints. This study contains an HTT analysis of 18 environmental chemicals with known liver toxicity. They were evaluated using male Sprague Dawley rats exposed to various concentrations daily for five consecutive days via oral gavage, with data collected on the sixth day. Here, we further explored the 5-day rat model to identify potential gene signatures that can differentiate between toxic and non-toxic liver responses and provide us with a potential histopathological endpoint of chemical exposure. We identified a distinct gene expression pattern that differentiated non-hepatotoxic compounds from hepatotoxic compounds in a dose-dependent manner, and an analysis of the significantly altered common genes indicated that toxic chemicals predominantly upregulated most of the genes and several pathways in amino acid and lipid metabolism. Finally, our liver injury module analysis revealed that several liver-toxic compounds showed similarities in the key injury phenotypes of cellular inflammation and proliferation, indicating potential molecular initiating processes that may lead to a specific end-stage liver disease.
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Affiliation(s)
- Venkat R. Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
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4
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Goel H, Printz RL, Shiota C, Estes SK, Pannala V, AbdulHameed MDM, Shiota M, Wallqvist A. Assessing Kidney Injury Induced by Mercuric Chloride in Guinea Pigs with In Vivo and In Vitro Experiments. Int J Mol Sci 2023; 24:7434. [PMID: 37108594 PMCID: PMC10138559 DOI: 10.3390/ijms24087434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Acute kidney injury, which is associated with high levels of morbidity and mortality, affects a significant number of individuals, and can be triggered by multiple factors, such as medications, exposure to toxic chemicals or other substances, disease, and trauma. Because the kidney is a critical organ, understanding and identifying early cellular or gene-level changes can provide a foundation for designing medical interventions. In our earlier work, we identified gene modules anchored to histopathology phenotypes associated with toxicant-induced liver and kidney injuries. Here, using in vivo and in vitro experiments, we assessed and validated these kidney injury-associated modules by analyzing gene expression data from the kidneys of male Hartley guinea pigs exposed to mercuric chloride. Using plasma creatinine levels and cell-viability assays as measures of the extent of renal dysfunction under in vivo and in vitro conditions, we performed an initial range-finding study to identify the appropriate doses and exposure times associated with mild and severe kidney injuries. We then monitored changes in kidney gene expression at the selected doses and time points post-toxicant exposure to characterize the mechanisms of kidney injury. Our injury module-based analysis revealed a dose-dependent activation of several phenotypic cellular processes associated with dilatation, necrosis, and fibrogenesis that were common across the experimental platforms and indicative of processes that initiate kidney damage. Furthermore, a comparison of activated injury modules between guinea pigs and rats indicated a strong correlation between the modules, highlighting their potential for cross-species translational studies.
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Affiliation(s)
- Himanshu Goel
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Richard L. Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chiyo Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Shanea K. Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Venkat Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Mohamed Diwan M. AbdulHameed
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
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Schyman P, Printz RL, Pannala VR, AbdulHameed MDM, Estes SK, Shiota C, Boyd KL, Shiota M, Wallqvist A. Genomics and metabolomics of early-stage thioacetamide-induced liver injury: An interspecies study between guinea pig and rat. Toxicol Appl Pharmacol 2021; 430:115713. [PMID: 34492290 PMCID: PMC8511347 DOI: 10.1016/j.taap.2021.115713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/10/2021] [Accepted: 09/02/2021] [Indexed: 12/27/2022]
Abstract
To study the complex processes involved in liver injuries, researchers rely on animal investigations, using chemically or surgically induced liver injuries, to extrapolate findings and infer human health risks. However, this presents obvious challenges in performing a detailed comparison and validation between the highly controlled animal models and development of liver injuries in humans. Furthermore, it is not clear whether there are species-dependent and -independent molecular initiating events or processes that cause liver injury before they eventually lead to end-stage liver disease. Here, we present a side-by-side study of rats and guinea pigs using thioacetamide to examine the similarities between early molecular initiating events during an acute-phase liver injury. We exposed Sprague Dawley rats and Hartley guinea pigs to a single dose of 25 or 100 mg/kg thioacetamide and collected blood plasma for metabolomic analysis and liver tissue for RNA-sequencing. The subsequent toxicogenomic analysis identified consistent liver injury trends in both genomic and metabolomic data within 24 and 33 h after thioacetamide exposure in rats and guinea pigs, respectively. In particular, we found species similarities in the key injury phenotypes of inflammation and fibrogenesis in our gene module analysis for liver injury phenotypes. We identified expression of several common genes (e.g., SPP1, TNSF18, SERPINE1, CLDN4, TIMP1, CD44, and LGALS3), activation of injury-specific KEGG pathways, and alteration of plasma metabolites involved in amino acid and bile acid metabolism as some of the key molecular processes that changed early upon thioacetamide exposure and could play a major role in the initiation of acute liver injury.
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Affiliation(s)
- Patric Schyman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Mohamed Diwan M AbdulHameed
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Chiyo Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelli Lynn Boyd
- Department of Pathology, Microbiology and Immunology, Division of Comparative Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA.
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6
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Miller CG, Henderson M, Mantopoulos D, Leskov I, Greco T, Schwarzbauer JE, Prenner JL. The Proteome of Preretinal Tissue in Proliferative Vitreoretinopathy. Ophthalmic Surg Lasers Imaging Retina 2021; 52:S5-S12. [PMID: 34310239 PMCID: PMC11299387 DOI: 10.3928/23258160-20210518-02] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND OBJECTIVE Proliferative vitreoretinopathy (PVR) is the leading cause of retinal detachment repair failure. However, the molecular pathogenesis remains incompletely understood. Determining the proteome of PVR will help to identify novel therapeutic targets. MATERIALS AND METHODS Preretinal tissue samples, delaminated during surgery from six PVR cases and one idiopathic epiretinal membrane (ERM) were analyzed by mass spectrometry. Tandem mass spectra were extracted using the UniProt database, generating a list of 896 proteins, which were subjected to pathway set and fold-change (ERM vs PVR) analyses. RESULTS Two pathways were enriched in PVR: extracellular matrix (ECM) organization and extracellular structure organization. A fold-change analysis comparing mean total spectral counts from PVR to an ERM control identified fibronectin, the ECM glycoprotein, as the protein most significantly elevated in PVR compared to ERM. CONCLUSION These data identify pathwayskey to PVR progression, including thoseinvolved in cell-mediated ECM assembly and thus tractional force generation at the cellular level. [Ophthalmic Surg Lasers Imaging Retina. 2021;52:S5-S12.].
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7
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Construction and Analysis of Survival-Associated Competing Endogenous RNA Network in Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4093426. [PMID: 33628780 PMCID: PMC7895565 DOI: 10.1155/2021/4093426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/31/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023]
Abstract
Increasing evidence has shown that noncoding RNAs play significant roles in the initiation, progression, and metastasis of tumours via participating in competing endogenous RNA (ceRNA) networks. However, the survival-associated ceRNA in lung adenocarcinoma (LUAD) remains poorly understood. In this study, we aimed to investigate the regulatory mechanisms underlying ceRNA in LUAD to identify novel prognostic factors. mRNA, lncRNA, and miRNA sequencing data obtained from the GDC data portal were utilized to identify differentially expressed (DE) RNAs. Survival-related RNAs were recognized using univariate Kaplan-Meier survival analysis. We performed functional enrichment analysis of survival-related mRNAs using the clusterProfiler package of R and STRING. lncRNA-miRNA and miRNA-mRNA interactions were predicted based on miRcode, Starbase, and miRanda. Subsequently, the survival-associated ceRNA network was constructed for LUAD. Multivariate Cox regression analysis was used to identify prognostic factors. Finally, we acquired 15 DE miRNAs, 49 DE lncRNAs, and 843 DE mRNAs associated with significant overall survival. Functional enrichment analysis indicated that survival-related DE mRNAs were enriched in cell cycle. The survival-associated lncRNA-miRNA-mRNA ceRNA network was constructed using five miRNAs, 49 mRNAs, and 21 lncRNAs. Furthermore, seven hub RNAs (LINC01936, miR-20a-5p, miR-31-5p, TNS1, TGFBR2, SMAD7, and NEDD4L) were identified based on the ceRNA network. LINC01936 and miR-31-5p were found to be significant using the multifactorial Cox regression model. In conclusion, we successfully constructed a survival-related lncRNA-miRNA-mRNA ceRNA regulatory network in LUAD and identified seven hub RNAs, which provide novel insights into the regulatory molecular mechanisms associated with survival of LUAD, and identified two independent prognostic predictors for LUAD.
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8
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Schyman P, Xu Z, Desai V, Wallqvist A. TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. Front Pharmacol 2021; 12:601511. [PMID: 33633572 PMCID: PMC7900624 DOI: 10.3389/fphar.2021.601511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/08/2021] [Indexed: 11/30/2022] Open
Abstract
Gene-set analysis is commonly used to identify trends in gene expression when cells, tissues, organs, or organisms are subjected to conditions that differ from those within the normal physiological range. However, tools for gene-set analysis to assess liver and kidney injury responses are less common. Furthermore, most websites for gene-set analysis lack the option for users to customize their gene-set database. Here, we present the ToxPanel website, which allows users to perform gene-set analysis to assess liver and kidney injuries using activation scores based on gene-expression fold-change values. The results are graphically presented to assess constituent injury phenotypes (histopathology), with interactive result tables that identify the main contributing genes to a given signal. In addition, ToxPanel offers the flexibility to analyze any set of custom genes based on gene fold-change values. ToxPanel is publically available online at https://toxpanel.bhsai.org. ToxPanel allows users to access our previously developed liver and kidney injury gene sets, which we have shown in previous work to yield robust results that correlate with the degree of injury. Users can also test and validate their customized gene sets using the ToxPanel website.
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Affiliation(s)
- Patric Schyman
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Zhen Xu
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Valmik Desai
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States
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9
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Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res 2021; 49:D605-D612. [PMID: 33237311 PMCID: PMC7779004 DOI: 10.1093/nar/gkaa1074] [Citation(s) in RCA: 3776] [Impact Index Per Article: 1258.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/20/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022] Open
Abstract
Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein–protein interactions are particularly important due to their versatility, specificity and adaptability. The STRING database aims to integrate all known and predicted associations between proteins, including both physical interactions as well as functional associations. To achieve this, STRING collects and scores evidence from a number of sources: (i) automated text mining of the scientific literature, (ii) databases of interaction experiments and annotated complexes/pathways, (iii) computational interaction predictions from co-expression and from conserved genomic context and (iv) systematic transfers of interaction evidence from one organism to another. STRING aims for wide coverage; the upcoming version 11.5 of the resource will contain more than 14 000 organisms. In this update paper, we describe changes to the text-mining system, a new scoring-mode for physical interactions, as well as extensive user interface features for customizing, extending and sharing protein networks. In addition, we describe how to query STRING with genome-wide, experimental data, including the automated detection of enriched functionalities and potential biases in the user's query data. The STRING resource is available online, at https://string-db.org/.
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Affiliation(s)
- Damian Szklarczyk
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Katerina C Nastou
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - David Lyon
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Rebecca Kirsch
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sampo Pyysalo
- TurkuNLP Group, Department of Future Technologies, University of Turku, 20014 Turun Yliopisto, Finland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Marc Legeay
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Tao Fang
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.,Department of Bioinformatics, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Karatzas E, Zachariou M, Bourdakou MM, Minadakis G, Oulas A, Kolios G, Delis A, Spyrou GM. PathWalks: identifying pathway communities using a disease-related map of integrated information. Bioinformatics 2020; 36:4070-4079. [PMID: 32369599 PMCID: PMC7332569 DOI: 10.1093/bioinformatics/btaa291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/11/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Understanding the underlying biological mechanisms and respective interactions of a disease remains an elusive, time consuming and costly task. Computational methodologies that propose pathway/mechanism communities and reveal respective relationships can be of great value as they can help expedite the process of identifying how perturbations in a single pathway can affect other pathways. RESULTS We present a random-walks-based methodology called PathWalks, where a walker crosses a pathway-to-pathway network under the guidance of a disease-related map. The latter is a gene network that we construct by integrating multi-source information regarding a specific disease. The most frequent trajectories highlight communities of pathways that are expected to be strongly related to the disease under study.We apply the PathWalks methodology on Alzheimer's disease and idiopathic pulmonary fibrosis and establish that it can highlight pathways that are also identified by other pathway analysis tools as well as are backed through bibliographic references. More importantly, PathWalks produces additional new pathways that are functionally connected with those already established, giving insight for further experimentation. AVAILABILITY AND IMPLEMENTATION https://github.com/vagkaratzas/PathWalks. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Evangelos Karatzas
- Department of Informatics and Telecommunications, University of Athens, Athens 15703, Greece
| | - Margarita Zachariou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Marilena M Bourdakou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,Department of Medicine, Laboratory of Pharmacology, Democritus University of Thrace, Komotini, Greece
| | - George Minadakis
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Anastasis Oulas
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - George Kolios
- Department of Medicine, Laboratory of Pharmacology, Democritus University of Thrace, Komotini, Greece
| | - Alex Delis
- Department of Informatics and Telecommunications, University of Athens, Athens 15703, Greece
| | - George M Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
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11
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Chase Huizar C, Raphael I, Forsthuber TG. Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis. Cell Immunol 2020; 358:104219. [PMID: 33039896 PMCID: PMC7927152 DOI: 10.1016/j.cellimm.2020.104219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disorder characterized by autoimmune-mediated inflammatory lesions in CNS leading to myelin damage and axonal loss. MS is a heterogenous disease with variable and unpredictable disease course. Due to its complex nature, MS is difficult to diagnose and responses to specific treatments may vary between individuals. Therefore, there is an indisputable need for biomarkers for early diagnosis, prediction of disease exacerbations, monitoring the progression of disease, and for measuring responses to therapy. Genomic and proteomic studies have sought to understand the molecular basis of MS and find biomarker candidates. Advances in next-generation sequencing and mass-spectrometry techniques have yielded an unprecedented amount of genomic and proteomic data; yet, translation of the results into the clinic has been underwhelming. This has prompted the development of novel data science techniques for exploring these large datasets to identify biologically relevant relationships and ultimately point towards useful biomarkers. Herein we discuss optimization of omics study designs, advances in the generation of omics data, and systems biology approaches aimed at improving biomarker discovery and translation to the clinic for MS.
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Affiliation(s)
- Carol Chase Huizar
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Itay Raphael
- Department of Neurological Surgery, University of Pittsburgh, UPMC Children's Hospital, Pittsburgh, PA, USA.
| | - Thomas G Forsthuber
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA.
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12
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Pannala VR, Estes SK, Rahim M, Trenary I, O’Brien TP, Shiota C, Printz RL, Reifman J, Shiota M, Young JD, Wallqvist A. Toxicant-Induced Metabolic Alterations in Lipid and Amino Acid Pathways Are Predictive of Acute Liver Toxicity in Rats. Int J Mol Sci 2020; 21:ijms21218250. [PMID: 33158035 PMCID: PMC7663358 DOI: 10.3390/ijms21218250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Liver disease and disorders associated with aberrant hepatocyte metabolism can be initiated via drug and environmental toxicant exposures. In this study, we tested the hypothesis that gene and metabolic profiling can reveal commonalities in liver response to different toxicants and provide the capability to identify early signatures of acute liver toxicity. We used Sprague Dawley rats and three classical hepatotoxicants: acetaminophen (2 g/kg), bromobenzene (0.4 g/kg), and carbon tetrachloride (0.3 g/kg), to identify early perturbations in liver metabolism after a single acute exposure dose. We measured changes in liver genes and plasma metabolites at two time points (5 and 10 h) and used genome-scale metabolic models to identify commonalities in liver responses across the three toxicants. We found strong correlations for gene and metabolic profiles between the toxicants, indicative of similarities in the liver response to toxicity. We identified several injury-specific pathways in lipid and amino acid metabolism that changed similarly across the three toxicants. Our findings suggest that several plasma metabolites in lipid and amino acid metabolism are strongly associated with the progression of liver toxicity, and as such, could be targeted and clinically assessed for their potential as early predictors of acute liver toxicity.
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Affiliation(s)
- Venkat R. Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
| | - Shanea K. Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
| | - Tracy P. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Chiyo Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Richard L. Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Jamey D. Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
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13
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Mechanism-based identification of plasma metabolites associated with liver toxicity. Toxicology 2020; 441:152493. [DOI: 10.1016/j.tox.2020.152493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 12/25/2022]
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14
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Pannala VR, Vinnakota KC, Estes SK, Trenary I, OˈBrien TP, Printz RL, Papin JA, Reifman J, Oyama T, Shiota M, Young JD, Wallqvist A. Genome-Scale Model-Based Identification of Metabolite Indicators for Early Detection of Kidney Toxicity. Toxicol Sci 2020; 173:293-312. [PMID: 31722432 PMCID: PMC8000070 DOI: 10.1093/toxsci/kfz228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Identifying early indicators of toxicant-induced organ damage is critical to provide effective treatment. To discover such indicators and the underlying mechanisms of toxicity, we used gentamicin as an exemplar kidney toxicant and performed systematic perturbation studies in Sprague Dawley rats. We obtained high-throughput data 7 and 13 h after administration of a single dose of gentamicin (0.5 g/kg) and identified global changes in genes in the liver and kidneys, metabolites in the plasma and urine, and absolute fluxes in central carbon metabolism. We used these measured changes in genes in the liver and kidney as constraints to a rat multitissue genome-scale metabolic network model to investigate the mechanism of gentamicin-induced kidney toxicity and identify metabolites associated with changes in tissue gene expression. Our experimental analysis revealed that gentamicin-induced metabolic perturbations could be detected as early as 7 h postexposure. Our integrated systems-level analyses suggest that changes in kidney gene expression drive most of the significant metabolite alterations in the urine. The analyses thus allowed us to identify several significantly enriched injury-specific pathways in the kidney underlying gentamicin-induced toxicity, as well as metabolites in these pathways that could serve as potential early indicators of kidney damage.
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Affiliation(s)
- Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817
| | - Kalyan C Vinnakota
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, Tennessee
| | - Tracy P OˈBrien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
| | - Tatsuya Oyama
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, Tennessee
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
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15
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Transcriptome meta-analysis reveals differences of immune profile between eutopic endometrium from stage I-II and III-IV endometriosis independently of hormonal milieu. Sci Rep 2020; 10:313. [PMID: 31941945 PMCID: PMC6962450 DOI: 10.1038/s41598-019-57207-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023] Open
Abstract
Eutopic endometrium appears to be crucial for endometriosis development. Despite of the evident importance, data regarding the cellular microenvironment remain unclear. Our objective was to explore the tissue microenvironment heterogeneity, transcripts, and pathways that are enriched in all phases of the menstrual cycle by analysing publicly deposited data derived from whole transcriptome microarrays of eutopic endometria of women with and without endometriosis. A meta-analysis of the transcriptome microarrays was performed using raw data available from a public database. Eligibility criteria included eutopic endometrium samples from women with endometriosis and healthy controls without any pathological condition reported the presence of an adequately reported normal menstrual phase, and samples containing both glandular and stromal components. Raw data were processed using a robust multiarray average method to provide background correction, normalisation, and summarisation. The batch effect was estimated by principal variant component analysis and removed using an empirical Bayes method. Cellular tissue heterogeneity was inferred using the xCell package. Differentially expressed genes were identified based on a 5% adjusted p value and a 2.0-fold change. Pathways were identified by functional enrichment based on the Molecular Signatures Database, a p value of < 5%, and an FDR q value of ≤ 25%. Genes that were more frequently found in pathways were identified using leading edge analysis. In a manner independent of cycle phase, the subpopulations of activated dendritic cells, CD4 T effector memory phenotype cells, eosinophils, macrophages M1, and natural killer T cells (NKT) were all higher in stage I-II endometriosis compared to those in healthy controls. The subpopulations of M2 macrophages and natural killer T cells were elevated in eutopic endometriums from women with stage III-IV endometriosis, and smooth muscle cells were always more prevalent in healthy eutopic endometriums. Among the differently expressed genes, FOS, FOSB, JUNB, and EGR1 were the most frequently mapped within the interaction networks, and this was independent of stage and cycle phase. The enriched pathways were directly related to immune surveillance, stem cell self-renewal, and epithelial mesenchymal transition. PI3K AKT mTOR, TGF signalling, and interferon alpha/gamma responses were enriched exclusively in stage III-IV endometriosis. The cellular microenvironments and immune cell profiles were different between eutopic endometriums from women with stage I-II and stage III-IV endometriosis, and these differences were independent of the hormonal milieu. Specifically, a pro-inflammatory profile was predominant in stage I-II endometriosis, and M1-M2 polarization into eutopic endometrium may be crucial for the progression of the disease. The higher prevalence of NKT cells in eutopic endometriums from women with endometriosis that was independent of cycle phase or staging suggested a sustained stress and/or damage to these eutopic endometriums. Based on this, the results of this meta-analysis are important for identifying challenges and opportunities for future research.
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16
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Zyla J, Marczyk M, Domaszewska T, Kaufmann SHE, Polanska J, Weiner J. Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. Bioinformatics 2019; 35:5146-5154. [PMID: 31165139 PMCID: PMC6954644 DOI: 10.1093/bioinformatics/btz447] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/08/2019] [Accepted: 06/10/2019] [Indexed: 01/12/2023] Open
Abstract
MOTIVATION Analysis of gene set (GS) enrichment is an essential part of functional omics studies. Here, we complement the established evaluation metrics of GS enrichment algorithms with a novel approach to assess the practical reproducibility of scientific results obtained from GS enrichment tests when applied to related data from different studies. RESULTS We evaluated eight established and one novel algorithm for reproducibility, sensitivity, prioritization, false positive rate and computational time. In addition to eight established algorithms, we also included Coincident Extreme Ranks in Numerical Observations (CERNO), a flexible and fast algorithm based on modified Fisher P-value integration. Using real-world datasets, we demonstrate that CERNO is robust to ranking metrics, as well as sample and GS size. CERNO had the highest reproducibility while remaining sensitive, specific and fast. In the overall ranking Pathway Analysis with Down-weighting of Overlapping Genes, CERNO and over-representation analysis performed best, while CERNO and GeneSetTest scored high in terms of reproducibility. AVAILABILITY AND IMPLEMENTATION tmod package implementing the CERNO algorithm is available from CRAN (cran.r-project.org/web/packages/tmod/index.html) and an online implementation can be found at http://tmod.online/. The datasets analyzed in this study are widely available in the KEGGdzPathwaysGEO, KEGGandMetacoreDzPathwaysGEO R package and GEO repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joanna Zyla
- Data Mining Group, Faculty of Automatic Control, Electronic and Computer Science, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Michal Marczyk
- Data Mining Group, Faculty of Automatic Control, Electronic and Computer Science, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
- Yale School of Medicine, Yale Cancer Center, New Haven, CT 06510, USA
| | - Teresa Domaszewska
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Joanna Polanska
- Data Mining Group, Faculty of Automatic Control, Electronic and Computer Science, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
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17
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Schyman P, Printz RL, Estes SK, O'Brien TP, Shiota M, Wallqvist A. Assessing Chemical-Induced Liver Injury In Vivo From In Vitro Gene Expression Data in the Rat: The Case of Thioacetamide Toxicity. Front Genet 2019; 10:1233. [PMID: 31850077 PMCID: PMC6901980 DOI: 10.3389/fgene.2019.01233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Consumers are exposed to thousands of chemicals with potentially adverse health effects. However, these chemicals will never be tested for toxicity because of the immense resources needed for animal-based (in vivo) toxicological studies. Today, there are no viable in vitro alternatives to these types of animal studies. To develop an in vitro approach, we investigated whether we could predict in vivo organ injuries in rats with the use of RNA-seq data acquired from tissues early in the development of toxicant-induced injury, by comparing gene expression data from RNA isolated from these rat tissues with those obtained from in vitro exposure of primary liver and kidney cells. We collected RNA-seq data from the liver and kidney tissues of Sprague-Dawley rats 8 or 24 h after exposing them to vehicle (control), low (25 mg/kg), or high (100 mg/kg) doses of thioacetamide, a known liver toxicant that promotes fibrosis; we used these doses and exposure times to cause only mild toxicant-induced injury. For the in vitro study, we treated two cell types from Sprague-Dawley rats, primary hepatocytes (vehicle; low, 0.025 mM; or high, 0.125 mM dose), and renal tube epithelial cells (vehicle; low, 0.125 mM; or high, 0.500 mM) dose) with the thioacetamide metabolite, thioacetamide-S-oxide, selecting in vitro doses and exposure times to recreate the early-stage toxicant-induced injury model that we achieved in vivo. RNA-seq data were collected 9 or 24 h after application of vehicle or thioacetamide-S-oxide. We found that our modular approach for the analysis of gene expression data derived from in vivo RNA-seq strongly correlated (R2 > 0.6) with the in vitro results at two different dose levels of thioacetamide/thioacetamide-S-oxide after 24 h of exposure. The top-ranked liver injury modules in vitro correctly identified the ensuing development of liver fibrosis.
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Affiliation(s)
- Patric Schyman
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc. (HJF), Bethesda, MD, United States
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States
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18
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Kalinin S, Meares GP, Lin SX, Pietruczyk EA, Saher G, Spieth L, Nave KA, Boullerne AI, Lutz SE, Benveniste EN, Feinstein DL. Liver kinase B1 depletion from astrocytes worsens disease in a mouse model of multiple sclerosis. Glia 2019; 68:600-616. [PMID: 31664743 PMCID: PMC7337013 DOI: 10.1002/glia.23742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/19/2019] [Accepted: 10/05/2019] [Indexed: 12/15/2022]
Abstract
Liver kinase B1 (LKB1) is a ubiquitously expressed kinase involved in the regulation of cell metabolism, growth, and inflammatory activation. We previously reported that a single nucleotide polymorphism in the gene encoding LKB1 is a risk factor for multiple sclerosis (MS). Since astrocyte activation and metabolic function have important roles in regulating neuroinflammation and neuropathology, we examined the serine/threonine kinase LKB1 in astrocytes in a chronic experimental autoimmune encephalomyelitis mouse model of MS. To reduce LKB1, a heterozygous astrocyte-selective conditional knockout (het-cKO) model was used. While disease incidence was similar, disease severity was worsened in het-cKO mice. RNAseq analysis identified Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched in het-cKO mice relating to mitochondrial function, confirmed by alterations in mitochondrial complex proteins and reductions in mRNAs related to astrocyte metabolism. Enriched pathways included major histocompatibility class II genes, confirmed by increases in MHCII protein in spinal cord and cerebellum of het-cKO mice. We observed increased numbers of CD4+ Th17 cells and increased neuronal damage in spinal cords of het-cKO mice, associated with reduced expression of choline acetyltransferase, accumulation of immunoglobulin-γ, and reduced expression of factors involved in motor neuron survival. In vitro, LKB1-deficient astrocytes showed reduced metabolic function and increased inflammatory activation. These data suggest that metabolic dysfunction in astrocytes, in this case due to LKB1 deficiency, can exacerbate demyelinating disease by loss of metabolic support and increase in the inflammatory environment.
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Affiliation(s)
- Sergey Kalinin
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Gordon P Meares
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, West Virginia
| | - Shao Xia Lin
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | | | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Gottingen, Germany
| | - Lena Spieth
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Gottingen, Germany
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Gottingen, Germany
| | - Anne I Boullerne
- Department of Anesthesiology, University of Illinois, Chicago, Illinois
| | - Sarah E Lutz
- Department of Anatomy and Cell Biology, University of Illinois, Chicago, Illinois
| | - Etty N Benveniste
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Douglas L Feinstein
- Department of Anesthesiology, University of Illinois, Chicago, Illinois.,Department of Veterans Affairs, Jesse Brown VA Medical Center, Chicago, Illinois
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19
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019. [PMID: 30476243 DOI: 10.1093/nar/gyk1131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
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Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.,Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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20
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019. [PMID: 30476243 DOI: 10.1093/nar/gky1131.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
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Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.,Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019; 47:D607-D613. [PMID: 30476243 PMCID: PMC6323986 DOI: 10.1093/nar/gky1131] [Citation(s) in RCA: 10254] [Impact Index Per Article: 2050.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/23/2018] [Accepted: 11/16/2018] [Indexed: 02/07/2023] Open
Abstract
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
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Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 where 1266=1266 or not 5936=5936-- qfcb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 where 9554=9554 and 1819=(select (case when (1819=1819) then 1819 else (select 4671 union select 3682) end))-- baqs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 8623=8623# mtsu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 8623=8623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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26
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 6143=8332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 where 7735=7735 or not 4799=3541-- rhxt] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 4781=(select (case when (4781=6244) then 4781 else (select 6244 union select 9918) end))-- lcaz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 or not 5936=5936-- miel] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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30
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 1819=(select (case when (1819=1819) then 1819 else (select 4671 union select 3682) end))-- qpln] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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31
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 or not 5936=5936# cpou] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 7833=4416-- xlsn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 where 9649=9649 and 2714=(select (case when (2714=6666) then 2714 else (select 6666 union select 4895) end))-- ejaf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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34
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 or not 5670=8100# fxoq] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 or not 6347=1706-- gnjn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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36
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 8623=8623-- yesg] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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37
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 and 2138=3169# zebx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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38
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 where 2289=2289 and 9793=8976-- mdxf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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39
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 where 1521=1521 and 8623=8623-- wmsp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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40
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 or not 4684=8950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering C. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2018. [DOI: 10.1093/nar/gky1131 or not 5936=5936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Annika L Gable
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - David Lyon
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stefan Wyder
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223 Madrid, Spain
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - John H Morris
- Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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Schyman P, Printz RL, Estes SK, Boyd KL, Shiota M, Wallqvist A. Identification of the Toxicity Pathways Associated With Thioacetamide-Induced Injuries in Rat Liver and Kidney. Front Pharmacol 2018; 9:1272. [PMID: 30459623 PMCID: PMC6232954 DOI: 10.3389/fphar.2018.01272] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/18/2018] [Indexed: 12/25/2022] Open
Abstract
Ingestion or exposure to chemicals poses a serious health risk. Early detection of cellular changes induced by such events is vital to identify appropriate countermeasures to prevent organ damage. We hypothesize that chemically induced organ injuries are uniquely associated with a set (module) of genes exhibiting significant changes in expression. We have previously identified gene modules specifically associated with organ injuries by analyzing gene expression levels in liver and kidney tissue from rats exposed to diverse chemical insults. Here, we assess and validate our injury-associated gene modules by analyzing gene expression data in liver, kidney, and heart tissues obtained from Sprague-Dawley rats exposed to thioacetamide, a known liver toxicant that promotes fibrosis. The rats were injected intraperitoneally with a low (25 mg/kg) or high (100 mg/kg) dose of thioacetamide for 8 or 24 h, and definite organ injury was diagnosed by histopathology. Injury-associated gene modules indicated organ injury specificity, with the liver being most affected by thioacetamide. The most activated liver gene modules were those associated with inflammatory cell infiltration and fibrosis. Previous studies on thioacetamide toxicity and our histological analyses supported these results, signifying the potential of gene expression data to identify organ injuries.
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Affiliation(s)
- Patric Schyman
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Kelli L Boyd
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, United States
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