1
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Douglass EF, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, Duran-Frigola M, Bertoni M, Badia-i-Mompel P, Mateo L, Guitart-Pla O, Chung V, Tang J, Zeng J, Aloy P, Saez-Rodriguez J, Guinney J, Gerhard DS, Califano A. A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. Cell Rep Med 2022; 3:100492. [PMID: 35106508 PMCID: PMC8784774 DOI: 10.1016/j.xcrm.2021.100492] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/08/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022]
Abstract
The Columbia Cancer Target Discovery and Development (CTD2) Center is developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA-seq) profiles of 25 cell lines perturbed with ∼400 clinical oncology drugs, to study a tumor-specific drug mechanism of action. Here, this resource serves as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions. Dose-response and perturbational profiles for 32 kinase inhibitors are provided to 21 teams who are blind to the identity of the compounds. The teams are asked to predict high-affinity binding targets of each compound among ∼1,300 targets cataloged in DrugBank. The best performing methods leverage gene expression profile similarity analysis as well as deep-learning methodologies trained on individual datasets. This study lays the foundation for future integrative analyses of pharmacogenomic data, reconciliation of polypharmacology effects in different tumor contexts, and insights into network-based assessments of drug mechanisms of action. Drug-perturbed RNA sequencing data can be used to identify drug targets Technology-based drug-target definitions often subsume literature definitions Literature and screening datasets provide complementary information on drug mechanisms
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Affiliation(s)
- Eugene F. Douglass
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA
- Pharmaceutical and Biomedical Sciences, University of Georgia, 250 W. Green Street, Athens, GA 30602, USA
| | - Robert J. Allaway
- Computational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA
| | - Bence Szalai
- Semmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary
| | - Wenyu Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tingzhong Tian
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Adrià Fernández-Torras
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Ron Realubit
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA
| | - Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alberto Pessia
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ziaurrehman Tanoli
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mohieddin Jafari
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fangping Wan
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Yuanpeng Xiong
- Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Miquel Duran-Frigola
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Martino Bertoni
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Pau Badia-i-Mompel
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Lídia Mateo
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Oriol Guitart-Pla
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Verena Chung
- Computational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA
| | | | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Justin Guinney
- Computational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA
- Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, 701 W 168th Street, New York, NY 10032, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY 10032, USA
- Corresponding author
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2
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Bertoni M, Duran-Frigola M, Badia-I-Mompel P, Pauls E, Orozco-Ruiz M, Guitart-Pla O, Alcalde V, Diaz VM, Berenguer-Llergo A, Brun-Heath I, Villegas N, de Herreros AG, Aloy P. Bioactivity descriptors for uncharacterized chemical compounds. Nat Commun 2021; 12:3932. [PMID: 34168145 PMCID: PMC8225676 DOI: 10.1038/s41467-021-24150-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 05/27/2021] [Indexed: 01/20/2023] Open
Abstract
Chemical descriptors encode the physicochemical and structural properties of small molecules, and they are at the core of chemoinformatics. The broad release of bioactivity data has prompted enriched representations of compounds, reaching beyond chemical structures and capturing their known biological properties. Unfortunately, bioactivity descriptors are not available for most small molecules, which limits their applicability to a few thousand well characterized compounds. Here we present a collection of deep neural networks able to infer bioactivity signatures for any compound of interest, even when little or no experimental information is available for them. Our signaturizers relate to bioactivities of 25 different types (including target profiles, cellular response and clinical outcomes) and can be used as drop-in replacements for chemical descriptors in day-to-day chemoinformatics tasks. Indeed, we illustrate how inferred bioactivity signatures are useful to navigate the chemical space in a biologically relevant manner, unveiling higher-order organization in natural product collections, and to enrich mostly uncharacterized chemical libraries for activity against the drug-orphan target Snail1. Moreover, we implement a battery of signature-activity relationship (SigAR) models and show a substantial improvement in performance, with respect to chemistry-based classifiers, across a series of biophysics and physiology activity prediction benchmarks.
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Affiliation(s)
- Martino Bertoni
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Miquel Duran-Frigola
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Ersilia Open Source Initiative, Cambridge, UK.
| | - Pau Badia-I-Mompel
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Eduardo Pauls
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Modesto Orozco-Ruiz
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Oriol Guitart-Pla
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Víctor Alcalde
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Víctor M Diaz
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) and Departament de Ciències de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
- Faculty of Medicine and Health Sciences, International University of Catalonia, Barcelona, Catalonia, Spain
| | - Antoni Berenguer-Llergo
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Isabelle Brun-Heath
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Núria Villegas
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) and Departament de Ciències de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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3
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Duran-Frigola M, Bertoni M, Blanco R, Martínez V, Pauls E, Alcalde V, Turon G, Villegas N, Fernández-Torras A, Pons C, Mateo L, Guitart-Pla O, Badia-i-Mompel P, Gimeno A, Soler N, Brun-Heath I, Zaragoza H, Aloy P. Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs. J Chem Inf Model 2020; 60:5730-5734. [PMID: 32672454 PMCID: PMC7370532 DOI: 10.1021/acs.jcim.0c00420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Indexed: 11/29/2022]
Abstract
Until a vaccine becomes available, the current repertoire of drugs is our only therapeutic asset to fight the SARS-CoV-2 outbreak. Indeed, emergency clinical trials have been launched to assess the effectiveness of many marketed drugs, tackling the decrease of viral load through several mechanisms. Here, we present an online resource, based on small-molecule bioactivity signatures and natural language processing, to expand the portfolio of compounds with potential to treat COVID-19. By comparing the set of drugs reported to be potentially active against SARS-CoV-2 to a universe of 1 million bioactive molecules, we identify compounds that display analogous chemical and functional features to the current COVID-19 candidates. Searches can be filtered by level of evidence and mechanism of action, and results can be restricted to drug molecules or include the much broader space of bioactive compounds. Moreover, we allow users to contribute COVID-19 drug candidates, which are automatically incorporated to the pipeline once per day. The computational platform, as well as the source code, is available at https://sbnb.irbbarcelona.org/covid19.
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Affiliation(s)
- Miquel Duran-Frigola
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Martino Bertoni
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Roi Blanco
- Amazon Search Science and
AI, 08018 Barcelona, Catalonia,
Spain
| | - Víctor Martínez
- Amazon Search Science and
AI, 08018 Barcelona, Catalonia,
Spain
| | - Eduardo Pauls
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Víctor Alcalde
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Gemma Turon
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Núria Villegas
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Adrià Fernández-Torras
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Carles Pons
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Lídia Mateo
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Oriol Guitart-Pla
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Pau Badia-i-Mompel
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Aleix Gimeno
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Nicolas Soler
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Isabelle Brun-Heath
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
| | - Hugo Zaragoza
- Amazon Search Science and
AI, 08018 Barcelona, Catalonia,
Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program
in Computational Biology, Institute for Research in Biomedicine
(IRB Barcelona), The Barcelona Institute of
Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona,
Catalonia, Spain
- Institució Catalana
de Recerca i Estudis Avançats (ICREA),
Passeig Lluís Companys, 23, 08010 Barcelona, Catalonia,
Spain
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4
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Mateo L, Guitart-Pla O, Pons C, Duran-Frigola M, Mosca R, Aloy P. A PanorOmic view of personal cancer genomes. Nucleic Acids Res 2019; 45:W195-W200. [PMID: 28453651 PMCID: PMC5570074 DOI: 10.1093/nar/gkx311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/12/2017] [Indexed: 12/02/2022] Open
Abstract
The massive molecular profiling of thousands of cancer patients has led to the identification of many tumor type specific driver genes. However, only a few (or none) of them are present in each individual tumor and, to enable precision oncology, we need to interpret the alterations found in a single patient. Cancer PanorOmics (http://panoromics.irbbarcelona.org) is a web-based resource to contextualize genomic variations detected in a personal cancer genome within the body of clinical and scientific evidence available for 26 tumor types, offering complementary cohort- and patient-centric views. Additionally, it explores the cellular environment of mutations by mapping them on the human interactome and providing quasi-atomic structural details, whenever available. This ‘PanorOmic’ molecular view of individual tumors, together with the appropriate genetic counselling and medical advice, should contribute to the identification of actionable alterations ultimately guiding the clinical decision-making process.
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Affiliation(s)
- Lidia Mateo
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain
| | - Oriol Guitart-Pla
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain
| | - Miquel Duran-Frigola
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain
| | - Roberto Mosca
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona 08028, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Catalonia, Spain
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5
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Abstract
Background The widespread incorporation of next-generation sequencing into clinical oncology has yielded an unprecedented amount of molecular data from thousands of patients. A main current challenge is to find out reliable ways to extrapolate results from one group of patients to another and to bring rationale to individual cases in the light of what is known from the cohorts. Results We present OncoGenomic Landscapes, a framework to analyze and display thousands of cancer genomic profiles in a 2D space. Our tool allows users to rapidly assess the heterogeneity of large cohorts, enabling the comparison to other groups of patients, and using driver genes as landmarks to aid in the interpretation of the landscapes. In our web-server, we also offer the possibility of mapping new samples and cohorts onto 22 predefined landscapes related to cancer cell line panels, organoids, patient-derived xenografts, and clinical tumor samples. Conclusions Contextualizing individual subjects in a more general landscape of human cancer is a valuable aid for basic researchers and clinical oncologists trying to identify treatment opportunities, maybe yet unapproved, for patients that ran out of standard therapeutic options. The web-server can be accessed at https://oglandscapes.irbbarcelona.org/. Electronic supplementary material The online version of this article (10.1186/s13073-018-0571-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lidia Mateo
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Oriol Guitart-Pla
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Miquel Duran-Frigola
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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6
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Gwinner F, Boulday G, Vandiedonck C, Arnould M, Cardoso C, Nikolayeva I, Guitart-Pla O, Denis CV, Christophe OD, Beghain J, Tournier-Lasserve E, Schwikowski B. Network-based analysis of omics data: the LEAN method. Bioinformatics 2017; 33:701-709. [PMID: 27797778 PMCID: PMC5408824 DOI: 10.1093/bioinformatics/btw676] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 10/25/2016] [Indexed: 12/20/2022] Open
Abstract
Motivation Most computational approaches for the analysis of omics data in the context of interaction networks have very long running times, provide single or partial, often heuristic, solutions and/or contain user-tuneable parameters. Results We introduce local enrichment analysis (LEAN) for the identification of dysregulated subnetworks from genome-wide omics datasets. By substituting the common subnetwork model with a simpler local subnetwork model, LEAN allows exact, parameter-free, efficient and exhaustive identification of local subnetworks that are statistically dysregulated, and directly implicates single genes for follow-up experiments. Evaluation on simulated and biological data suggests that LEAN generally detects dysregulated subnetworks better, and reflects biological similarity between experiments more clearly than standard approaches. A strong signal for the local subnetwork around Von Willebrand Factor (VWF), a gene which showed no change on the mRNA level, was identified by LEAN in transcriptome data in the context of the genetic disease Cerebral Cavernous Malformations (CCM). This signal was experimentally found to correspond to an unexpected strong cellular effect on the VWF protein. LEAN can be used to pinpoint statistically significant local subnetworks in any genome-scale dataset. Availability and Implementation The R-package LEANR implementing LEAN is supplied as supplementary material and available on CRAN (https://cran.r-project.org). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Frederik Gwinner
- Univ Paris Diderot, Sorbonne Paris Cité, UMRS 1161, F-75010 Paris, France.,INSERM, U1161, F-75010 Paris, France
| | - Gwénola Boulday
- Univ Paris Diderot, Sorbonne Paris Cité, UMRS 1161, F-75010 Paris, France.,INSERM, U1161, F-75010 Paris, France
| | - Claire Vandiedonck
- Univ Paris Diderot, Sorbonne Paris Cité, UMRS 958, F-75010 Paris, France.,INSERM, U958, F-75010 Paris, France
| | - Minh Arnould
- Univ Paris Diderot, Sorbonne Paris Cité, UMRS 1161, F-75010 Paris, France.,INSERM, U1161, F-75010 Paris, France
| | - Cécile Cardoso
- Univ Paris Diderot, Sorbonne Paris Cité, UMRS 1161, F-75010 Paris, France.,INSERM, U1161, F-75010 Paris, France
| | - Iryna Nikolayeva
- Systems Biology Lab, C3BI, USR 3756, Institut Pasteur/CNRS, Institut Pasteur, F-75015 Paris, France.,Functional Genetics of Infectious Diseases Unit, Institut Pasteur, F-75015 Paris, France.,Univ Paris-Descartes, Sorbonne Paris Cité, F-75006 Paris, France
| | - Oriol Guitart-Pla
- Systems Biology Lab, C3BI, USR 3756, Institut Pasteur/CNRS, Institut Pasteur, F-75015 Paris, France
| | - Cécile V Denis
- Unité 1176, INSERM, Univ Paris-Sud, Université Paris-Saclay, F-94270 Le Kremlin-Bicêtre, France
| | - Olivier D Christophe
- Unité 1176, INSERM, Univ Paris-Sud, Université Paris-Saclay, F-94270 Le Kremlin-Bicêtre, France
| | - Johann Beghain
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, F-75015 Paris, France.,Genetics and Genomics of Insect Vectors, Institut Pasteur, F-75015 Paris, France
| | - Elisabeth Tournier-Lasserve
- Univ Paris Diderot, Sorbonne Paris Cité, UMRS 1161, F-75010 Paris, France.,INSERM, U1161, F-75010 Paris, France.,AP-HP, Groupe Hospitalier Saint-Louis Lariboisière-Fernand-Widal, F-75010 Paris, France
| | - Benno Schwikowski
- Systems Biology Lab, C3BI, USR 3756, Institut Pasteur/CNRS, Institut Pasteur, F-75015 Paris, France
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7
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Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B. The Cyni framework for network inference in Cytoscape. Bioinformatics 2014; 31:1499-501. [PMID: 25527096 DOI: 10.1093/bioinformatics/btu812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/04/2014] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Research on methods for the inference of networks from biological data is making significant advances, but the adoption of network inference in biomedical research practice is lagging behind. Here, we present Cyni, an open-source 'fill-in-the-algorithm' framework that provides common network inference functionality and user interface elements. Cyni allows the rapid transformation of Java-based network inference prototypes into apps of the popular open-source Cytoscape network analysis and visualization ecosystem. Merely placing the resulting app in the Cytoscape App Store makes the method accessible to a worldwide community of biomedical researchers by mouse click. In a case study, we illustrate the transformation of an ARACNE implementation into a Cytoscape app. AVAILABILITY AND IMPLEMENTATION Cyni, its apps, user guides, documentation and sample code are available from the Cytoscape App Store http://apps.cytoscape.org/apps/cynitoolbox CONTACT benno.schwikowski@pasteur.fr.
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Affiliation(s)
- Oriol Guitart-Pla
- Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Manjunath Kustagi
- Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Frank Rügheimer
- Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Andrea Califano
- Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Benno Schwikowski
- Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA
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