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Liu X, Tao Y, Cai Z, Bao P, Ma H, Li K, Li M, Zhu Y, Lu ZJ. Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data. Bioinformatics 2024; 40:btae316. [PMID: 38741230 PMCID: PMC11139513 DOI: 10.1093/bioinformatics/btae316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/29/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024] Open
Abstract
MOTIVATION Multi-omics data provide a comprehensive view of gene regulation at multiple levels, which is helpful in achieving accurate diagnosis of complex diseases like cancer. However, conventional integration methods rarely utilize prior biological knowledge and lack interpretability. RESULTS To integrate various multi-omics data of tissue and liquid biopsies for disease diagnosis and prognosis, we developed a biological pathway informed Transformer, Pathformer. It embeds multi-omics input with a compacted multi-modal vector and a pathway-based sparse neural network. Pathformer also leverages criss-cross attention mechanism to capture the crosstalk between different pathways and modalities. We first benchmarked Pathformer with 18 comparable methods on multiple cancer datasets, where Pathformer outperformed all the other methods, with an average improvement of 6.3%-14.7% in F1 score for cancer survival prediction, 5.1%-12% for cancer stage prediction, and 8.1%-13.6% for cancer drug response prediction. Subsequently, for cancer prognosis prediction based on tissue multi-omics data, we used a case study to demonstrate the biological interpretability of Pathformer by identifying key pathways and their biological crosstalk. Then, for cancer early diagnosis based on liquid biopsy data, we used plasma and platelet datasets to demonstrate Pathformer's potential of clinical applications in cancer screening. Moreover, we revealed deregulation of interesting pathways (e.g. scavenger receptor pathway) and their crosstalk in cancer patients' blood, providing potential candidate targets for cancer microenvironment study. AVAILABILITY AND IMPLEMENTATION Pathformer is implemented and freely available at https://github.com/lulab/Pathformer.
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Affiliation(s)
- Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Zilin Cai
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Hongli Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Kexing Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), MST State Key Laboratory of Complex Severe and Rare Diseases, MOE Key Laboratory of Rheumatology and Clinical Immunology, Beijing 100730, China
| | - Yunping Zhu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
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Buzzao D, Castresana-Aguirre M, Guala D, Sonnhammer ELL. Benchmarking enrichment analysis methods with the disease pathway network. Brief Bioinform 2024; 25:bbae069. [PMID: 38436561 PMCID: PMC10939300 DOI: 10.1093/bib/bbae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/10/2024] [Accepted: 02/03/2024] [Indexed: 03/05/2024] Open
Abstract
Enrichment analysis (EA) is a common approach to gain functional insights from genome-scale experiments. As a consequence, a large number of EA methods have been developed, yet it is unclear from previous studies which method is the best for a given dataset. The main issues with previous benchmarks include the complexity of correctly assigning true pathways to a test dataset, and lack of generality of the evaluation metrics, for which the rank of a single target pathway is commonly used. We here provide a generalized EA benchmark and apply it to the most widely used EA methods, representing all four categories of current approaches. The benchmark employs a new set of 82 curated gene expression datasets from DNA microarray and RNA-Seq experiments for 26 diseases, of which only 13 are cancers. In order to address the shortcomings of the single target pathway approach and to enhance the sensitivity evaluation, we present the Disease Pathway Network, in which related Kyoto Encyclopedia of Genes and Genomes pathways are linked. We introduce a novel approach to evaluate pathway EA by combining sensitivity and specificity to provide a balanced evaluation of EA methods. This approach identifies Network Enrichment Analysis methods as the overall top performers compared with overlap-based methods. By using randomized gene expression datasets, we explore the null hypothesis bias of each method, revealing that most of them produce skewed P-values.
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Affiliation(s)
- Davide Buzzao
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 171 21 Solna, Sweden
| | | | - Dimitri Guala
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 171 21 Solna, Sweden
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 171 21 Solna, Sweden
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Nagasubramanian K, Gupta K. Interactome analysis implicates class II transactivator (CIITA) in depression and other neuroinflammatory disorders. Int J Neurosci 2023:1-19. [PMID: 37933915 DOI: 10.1080/00207454.2023.2279502] [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: 08/02/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
PURPOSE Inappropriate inflammatory responses within the nervous system (neuroinflammation) have been implicated in several neurological conditions. Class II transactivator (CIITA), a principal regulator of the major histocompatibility complex II (MHCII), is known to play essential roles in inflammation. Hence, CIITA and its interactors could be potentially involved in multiple neurological disorders. However, the molecular mechanisms underlying CIITA-mediated neuroinflammation (NI) are yet to be understood. MATERIALS AND METHODS In this regard, we analyzed the potential involvement of CIITA and its interactome in the regulation of neuroinflammation. In the present study, using various computational tools, we aimed (1) to identify NI-related proteins, (2) to filter the critical interactors in the CIITA-NI network, and (3) to analyze the protein-disease interactions and the associated molecular pathways through which CIITA could influence neuroinflammation. RESULTS CIITA was found to interact with P T GS2, GSK3B, and NR3C1 and may influence depressive disorders. Further, the IL4/IL13 pathway was found to be potentially underlying the CIITA-interactomemediated effects on neurological disorders. Moreover, CIITA was found to be connected to genes associated with depressive disorder through IL4, wherein CIITA was found to be potentially involved in depressive disorders through IL-4/IL-13 and hippo pathways. However, the present study is based on the existing data on protein interactomes and could be re-evaluated as newer interactions are discovered. Also, the functional mechanisms of CIITA's roles in neuroinflammation must be evaluated further. CONCLUSION Notwithstanding these limitations, the results presented here, could form a basis for further experimental studies to assess CIITA as a potential therapeutic target in managing depression and other neuroinflammatory disorders.
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Affiliation(s)
- Kishore Nagasubramanian
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
| | - Krishnakant Gupta
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, India
- NCCS, Pune, India
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Windels SFL, Malod-Dognin N, Pržulj N. Identifying cellular cancer mechanisms through pathway-driven data integration. Bioinformatics 2022; 38:4344-4351. [PMID: 35916710 PMCID: PMC9477533 DOI: 10.1093/bioinformatics/btac493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/14/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Cancer is a genetic disease in which accumulated mutations of driver genes induce a functional reorganization of the cell by reprogramming cellular pathways. Current approaches identify cancer pathways as those most internally perturbed by gene expression changes. However, driver genes characteristically perform hub roles between pathways. Therefore, we hypothesize that cancer pathways should be identified by changes in their pathway-pathway relationships. RESULTS To learn an embedding space that captures the relationships between pathways in a healthy cell, we propose pathway-driven non-negative matrix tri-factorization. In this space, we determine condition-specific (i.e. diseased and healthy) embeddings of pathways and genes. Based on these embeddings, we define our 'NMTF centrality' to measure a pathway's or gene's functional importance, and our 'moving distance', to measure the change in its functional relationships. We combine both measures to predict 15 genes and pathways involved in four major cancers, predicting 60 gene-cancer associations in total, covering 28 unique genes. To further exploit driver genes' tendency to perform hub roles, we model our network data using graphlet adjacency, which considers nodes adjacent if their interaction patterns form specific shapes (e.g. paths or triangles). We find that the predicted genes rewire pathway-pathway interactions in the immune system and provide literary evidence that many are druggable (15/28) and implicated in the associated cancers (47/60). We predict six druggable cancer-specific drug targets. AVAILABILITY AND IMPLEMENTATION The code and data are available at: https://gitlab.bsc.es/swindels/pathway_driven_nmtf. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sam F L Windels
- Department of Computer Science, University College London, London WC1E 6BT, UK,Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Noël Malod-Dognin
- Department of Computer Science, University College London, London WC1E 6BT, UK,Barcelona Supercomputing Center, 08034 Barcelona, Spain
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Wang S, Zheng H, Choi JS, Lee JK, Li X, Hu H. A systematic evaluation of the computational tools for ligand-receptor-based cell-cell interaction inference. Brief Funct Genomics 2022; 21:339-356. [PMID: 35822343 PMCID: PMC9479691 DOI: 10.1093/bfgp/elac019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-cell interactions (CCIs) are essential for multicellular organisms to coordinate biological processes and functions. One classical type of CCI interaction is between secreted ligands and cell surface receptors, i.e. ligand-receptor (LR) interactions. With the recent development of single-cell technologies, a large amount of single-cell ribonucleic acid (RNA) sequencing (scRNA-Seq) data has become widely available. This data availability motivated the single-cell-resolution study of CCIs, particularly LR-based CCIs. Dozens of computational methods and tools have been developed to predict CCIs by identifying LR-based CCIs. Many of these tools have been theoretically reviewed. However, there is little study on current LR-based CCI prediction tools regarding their performance and running results on public scRNA-Seq datasets. In this work, to fill this gap, we tested and compared nine of the most recent computational tools for LR-based CCI prediction. We used 15 well-studied scRNA-Seq samples that correspond to approximately 100K single cells under different experimental conditions for testing and comparison. Besides briefing the methodology used in these nine tools, we summarized the similarities and differences of these tools in terms of both LR prediction and CCI inference between cell types. We provided insight into using these tools to make meaningful discoveries in understanding cell communications.
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Affiliation(s)
| | | | | | | | - Xiaoman Li
- Corresponding authors: Haiyan Hu, Department of Computer Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078820134; Fax: +1-4078235835; E-mail: ; Xiaoman Li, Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078234811; Fax: +1-4078235835; E-mail:
| | - Haiyan Hu
- Corresponding authors: Haiyan Hu, Department of Computer Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078820134; Fax: +1-4078235835; E-mail: ; Xiaoman Li, Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078234811; Fax: +1-4078235835; E-mail:
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Aguilar D, Bosacoma A, Blanco I, Tura-Ceide O, Serrano-Mollar A, Barberà JA, Peinado VI. Differences and Similarities between the Lung Transcriptomic Profiles of COVID-19, COPD, and IPF Patients: A Meta-Analysis Study of Pathophysiological Signaling Pathways. Life (Basel) 2022; 12:887. [PMID: 35743918 PMCID: PMC9227224 DOI: 10.3390/life12060887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 06/11/2022] [Indexed: 11/20/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic respiratory disease associated with high morbidity and mortality. Although many patients recover, long-term sequelae after infection have become increasingly recognized and concerning. Among other sequelae, the available data indicate that many patients who recover from COVID-19 could develop fibrotic abnormalities over time. To understand the basic pathophysiology underlying the development of long-term pulmonary fibrosis in COVID-19, as well as the higher mortality rates in patients with pre-existing lung diseases, we compared the transcriptomic fingerprints among patients with COVID-19, idiopathic pulmonary fibrosis (IPF), and chronic obstructive pulmonary disease (COPD) using interactomic analysis. Patients who died of COVID-19 shared some of the molecular biological processes triggered in patients with IPF, such as those related to immune response, airway remodeling, and wound healing, which could explain the radiological images seen in some patients after discharge. However, other aspects of this transcriptomic profile did not resemble the profile associated with irreversible fibrotic processes in IPF. Our mathematical approach instead showed that the molecular processes that were altered in COVID-19 patients more closely resembled those observed in COPD. These data indicate that patients with COPD, who have overcome COVID-19, might experience a faster decline in lung function that will undoubtedly affect global health.
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Affiliation(s)
- Daniel Aguilar
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREDH), 28005 Madrid, Spain;
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (A.B.); (I.B.); (O.T.-C.); (A.S.-M.); (J.A.B.)
| | - Adelaida Bosacoma
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (A.B.); (I.B.); (O.T.-C.); (A.S.-M.); (J.A.B.)
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Isabel Blanco
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (A.B.); (I.B.); (O.T.-C.); (A.S.-M.); (J.A.B.)
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Department of Pulmonary Medicine, Hospital Clínic, University of Barcelona, 08007 Barcelona, Spain
| | - Olga Tura-Ceide
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (A.B.); (I.B.); (O.T.-C.); (A.S.-M.); (J.A.B.)
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Department of Pulmonary Medicine, Hospital Clínic, University of Barcelona, 08007 Barcelona, Spain
- Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
| | - Anna Serrano-Mollar
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (A.B.); (I.B.); (O.T.-C.); (A.S.-M.); (J.A.B.)
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Department of Experimental Pathology, Institut d’Investigacions Biomèdiques de Barcelona (IIBB), CSIC-IDIBAPS, 08036 Barcelona, Spain
| | - Joan Albert Barberà
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (A.B.); (I.B.); (O.T.-C.); (A.S.-M.); (J.A.B.)
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Department of Pulmonary Medicine, Hospital Clínic, University of Barcelona, 08007 Barcelona, Spain
| | - Victor Ivo Peinado
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (A.B.); (I.B.); (O.T.-C.); (A.S.-M.); (J.A.B.)
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Department of Pulmonary Medicine, Hospital Clínic, University of Barcelona, 08007 Barcelona, Spain
- Department of Experimental Pathology, Institut d’Investigacions Biomèdiques de Barcelona (IIBB), CSIC-IDIBAPS, 08036 Barcelona, Spain
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Castresana-Aguirre M, Guala D, Sonnhammer ELL. Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis. Front Genet 2022; 13:855766. [PMID: 35620466 PMCID: PMC9127507 DOI: 10.3389/fgene.2022.855766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Functional analysis of gene sets derived from experiments is typically done by pathway annotation. Although many algorithms exist for analyzing the association between a gene set and a pathway, an issue which is generally ignored is that gene sets often represent multiple pathways. In such cases an association to a pathway is weakened by the presence of genes associated with other pathways. A way to counteract this is to cluster the gene set into more homogenous parts before performing pathway analysis on each module. We explored whether network-based pre-clustering of a query gene set can improve pathway analysis. The methods MCL, Infomap, and MGclus were used to cluster the gene set projected onto the FunCoup network. We characterized how well these methods are able to detect individual pathways in multi-pathway gene sets, and applied each of the clustering methods in combination with four pathway analysis methods: Gene Enrichment Analysis, BinoX, NEAT, and ANUBIX. Using benchmarks constructed from the KEGG pathway database we found that clustering can be beneficial by increasing the sensitivity of pathway analysis methods and by providing deeper insights of biological mechanisms related to the phenotype under study. However, keeping a high specificity is a challenge. For ANUBIX, clustering caused a minor loss of specificity, while for BinoX and NEAT it caused an unacceptable loss of specificity. GEA had very low sensitivity both before and after clustering. The choice of clustering method only had a minor effect on the results. We show examples of this approach and conclude that clustering can improve overall pathway annotation performance, but should only be used if the used enrichment method has a low false positive rate.
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Affiliation(s)
| | | | - Erik L. L. Sonnhammer
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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Song C, Zhang J, Liu Y, Hu Y, Feng C, Shi P, Zhang Y, Wang L, Xie Y, Zhang M, Zhao X, Cao Y, Li C, Sun H. Characterization and Validation of ceRNA-Mediated Pathway–Pathway Crosstalk Networks Across Eight Major Cardiovascular Diseases. Front Cell Dev Biol 2022; 10:762129. [PMID: 35433687 PMCID: PMC9010821 DOI: 10.3389/fcell.2022.762129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 03/01/2022] [Indexed: 01/08/2023] Open
Abstract
Pathway analysis is considered as an important strategy to reveal the underlying mechanisms of diseases. Pathways that are involved in crosstalk can regulate each other and co-regulate downstream biological processes. Furthermore, some genes in the pathways can function with other genes via the relationship of the competing endogenous RNA (ceRNA) mechanism, which has also been demonstrated to play key roles in cellular biology. However, the comprehensive analysis of ceRNA-mediated pathway crosstalk is lacking. Here, we constructed the landscape of the ceRNA-mediated pathway–pathway crosstalk of eight major cardiovascular diseases (CVDs) based on sequencing data from ∼2,800 samples. Some common features shared by numerous CVDs were uncovered. A fraction of the pathway–pathway crosstalk was conserved in multiple CVDs and a core pathway–pathway crosstalk network was identified, suggesting the similarity of pathway–pathway crosstalk among CVDs. Experimental evidence also demonstrated that the pathway crosstalk was functioned in CVDs. We split all hub pathways of each pathway–pathway crosstalk network into three categories, namely, common hubs, differential hubs, and specific hubs, which could highlight the common or specific biological mechanisms. Importantly, after a comparison analysis of the hub pathways of networks, ∼480 hub pathway-induced common modules were identified to exert functions in CVDs broadly. Moreover, we performed a random walk algorithm on the hub pathway-induced sub-network and identified 23 potentially novel CVD-related pathways. In summary, our study revealed the potential molecular regulatory mechanisms of ceRNA crosstalk in pathway–pathway crosstalk levels and provided a novel routine to investigate the pathway–pathway crosstalk in cardiology. All CVD pathway–pathway crosstalks are provided in http://www.licpathway.net/cepathway/index.html.
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Affiliation(s)
- Chao Song
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Jian Zhang
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Yongsheng Liu
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Yinling Hu
- Department of Rehabilitation, Beijing Rehabilitation Hospital of Capital Medical University, Beijing, China
| | - Chenchen Feng
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Pilong Shi
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Yuexin Zhang
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Lixin Wang
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Yawen Xie
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Meitian Zhang
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Xilong Zhao
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Yonggang Cao
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Chunquan Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
- *Correspondence: Hongli Sun, ; Chunquan Li,
| | - Hongli Sun
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
- *Correspondence: Hongli Sun, ; Chunquan Li,
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Ogris C, Castresana-Aguirre M, Sonnhammer ELL. PathwAX II: Network-based pathway analysis with interactive visualization of network crosstalk. Bioinformatics 2022; 38:2659-2660. [PMID: 35266519 PMCID: PMC9048662 DOI: 10.1093/bioinformatics/btac153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/03/2022] [Accepted: 03/09/2022] [Indexed: 11/28/2022] Open
Abstract
Motivation Pathway annotation tools are indispensable for the interpretation of a wide range of experiments in life sciences. Network-based algorithms have recently been developed which are more sensitive than traditional overlap-based algorithms, but there is still a lack of good online tools for network-based pathway analysis. Results We present PathwAX II—a pathway analysis web tool based on network crosstalk analysis using the BinoX algorithm. It offers several new features compared with the first version, including interactive graphical network visualization of the crosstalk between a query gene set and an enriched pathway, and the addition of Reactome pathways. Availability and implementation PathwAX II is available at http://pathwax.sbc.su.se. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christoph Ogris
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17121 Solna, Box, Sweden 1031.,Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany Ingolstädter Landstr. 1 85764
| | - Miguel Castresana-Aguirre
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17121 Solna, Box, Sweden 1031
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, 17121 Solna, Box, Sweden 1031
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Guala D, Sonnhammer ELL. Network Crosstalk as a Basis for Drug Repurposing. Front Genet 2022; 13:792090. [PMID: 35350247 PMCID: PMC8958038 DOI: 10.3389/fgene.2022.792090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 01/27/2022] [Indexed: 11/23/2022] Open
Abstract
The need for systematic drug repurposing has seen a steady increase over the past decade and may be particularly valuable to quickly remedy unexpected pandemics. The abundance of functional interaction data has allowed mapping of substantial parts of the human interactome modeled using functional association networks, favoring network-based drug repurposing. Network crosstalk-based approaches have never been tested for drug repurposing despite their success in the related and more mature field of pathway enrichment analysis. We have, therefore, evaluated the top performing crosstalk-based approaches for drug repurposing. Additionally, the volume of new interaction data as well as more sophisticated network integration approaches compelled us to construct a new benchmark for performance assessment of network-based drug repurposing tools, which we used to compare network crosstalk-based methods with a state-of-the-art technique. We find that network crosstalk-based drug repurposing is able to rival the state-of-the-art method and in some cases outperform it.
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Affiliation(s)
- Dimitri Guala
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
- Merck AB, Solna, Sweden
| | - Erik L. L. Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
- *Correspondence: Erik L. L. Sonnhammer,
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Castresana-Aguirre M, Persson E, Sonnhammer ELL. PathBIX-a web server for network-based pathway annotation with adaptive null models. BIOINFORMATICS ADVANCES 2021; 1:vbab010. [PMID: 36700096 PMCID: PMC9710673 DOI: 10.1093/bioadv/vbab010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/30/2021] [Indexed: 01/28/2023]
Abstract
Motivation Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, utilize biological networks to gain a richer source of information as a basis of the analysis than merely the gene content. Network-based methods use the network crosstalk between the query gene set and the genes in known pathways, and compare this to a null model of random expectation. Results We developed PathBIX, a novel web application for network-based pathway analysis, based on the recently published ANUBIX algorithm which has been shown to be more accurate than previous network-based methods. The PathBIX website performs pathway annotation for 21 species, and utilizes prefetched and preprocessed network data from FunCoup 5.0 networks and pathway data from three databases: KEGG, Reactome, and WikiPathways. Availability https://pathbix.sbc.su.se/. Contact erik.sonnhammer@scilifelab.se. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Miguel Castresana-Aguirre
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 17121, Sweden
| | - Emma Persson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 17121, Sweden
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 17121, Sweden,To whom correspondence should be addressed.
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12
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Reimegård J, Tarbier M, Danielsson M, Schuster J, Baskaran S, Panagiotou S, Dahl N, Friedländer MR, Gallant CJ. A combined approach for single-cell mRNA and intracellular protein expression analysis. Commun Biol 2021; 4:624. [PMID: 34035432 PMCID: PMC8149646 DOI: 10.1038/s42003-021-02142-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/30/2021] [Indexed: 01/28/2023] Open
Abstract
Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation. Here, the authors present SPARC, a scalable approach for simultaneously measuring mRNA expression levels and targeted intracellular protein levels in single cells. They use SPARC to measure dynamic expression changes in human cells during neuronal differentiation and show that mRNA levels are poor predictors of protein abundances and activity in individual cells, indicating that the measurements are complementary.
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Affiliation(s)
- Johan Reimegård
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marcus Danielsson
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jens Schuster
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sathishkumar Baskaran
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Styliani Panagiotou
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Caroline J Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. .,10x Genomics, Stockholm, Sweden.
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13
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Ogris C, Hu Y, Arloth J, Müller NS. Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data. Sci Rep 2021; 11:6806. [PMID: 33762588 PMCID: PMC7990936 DOI: 10.1038/s41598-021-85544-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/04/2021] [Indexed: 12/28/2022] Open
Abstract
Constantly decreasing costs of high-throughput profiling on many molecular levels generate vast amounts of multi-omics data. Studying one biomedical question on two or more omic levels provides deeper insights into underlying molecular processes or disease pathophysiology. For the majority of multi-omics data projects, the data analysis is performed level-wise, followed by a combined interpretation of results. Hence the full potential of integrated data analysis is not leveraged yet, presumably due to the complexity of the data and the lacking toolsets. We propose a versatile approach, to perform a multi-level fully integrated analysis: The Knowledge guIded Multi-Omics Network inference approach, KiMONo (https://github.com/cellmapslab/kimono). KiMONo performs network inference by using statistical models for combining omics measurements coupled to a powerful knowledge-guided strategy exploiting prior information from existing biological sources. Within the resulting multimodal network, nodes represent features of all input types e.g. variants and genes while edges refer to knowledge-supported and statistically derived associations. In a comprehensive evaluation, we show that our method is robust to noise and exemplify the general applicability to the full spectrum of multi-omics data, demonstrating that KiMONo is a powerful approach towards leveraging the full potential of data sets for detecting biomarker candidates.
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Affiliation(s)
- Christoph Ogris
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Yue Hu
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Janine Arloth
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Translational Psychiatry, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Nikola S Müller
- Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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14
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Acevedo N, Scala G, Merid SK, Frumento P, Bruhn S, Andersson A, Ogris C, Bottai M, Pershagen G, Koppelman GH, Melén E, Sonnhammer E, Alm J, Söderhäll C, Kere J, Greco D, Scheynius A. DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life. Int J Mol Sci 2021; 22:ijms22020801. [PMID: 33466918 PMCID: PMC7830007 DOI: 10.3390/ijms22020801] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/23/2022] Open
Abstract
DNA methylation changes may predispose becoming IgE-sensitized to allergens. We analyzed whether DNA methylation in peripheral blood mononuclear cells (PBMC) is associated with IgE sensitization at 5 years of age (5Y). DNA methylation was measured in 288 PBMC samples from 74 mother/child pairs from the birth cohort ALADDIN (Assessment of Lifestyle and Allergic Disease During INfancy) using the HumanMethylation450BeadChip (Illumina). PBMCs were obtained from the mothers during pregnancy and from their children in cord blood, at 2 years and 5Y. DNA methylation levels at each time point were compared between children with and without IgE sensitization to allergens at 5Y. For replication, CpG sites associated with IgE sensitization in ALADDIN were evaluated in whole blood DNA of 256 children, 4 years old, from the BAMSE (Swedish abbreviation for Children, Allergy, Milieu, Stockholm, Epidemiology) cohort. We found 34 differentially methylated regions (DMRs) associated with IgE sensitization to airborne allergens and 38 DMRs associated with sensitization to food allergens in children at 5Y (Sidak p ≤ 0.05). Genes associated with airborne sensitization were enriched in the pathway of endocytosis, while genes associated with food sensitization were enriched in focal adhesion, the bacterial invasion of epithelial cells, and leukocyte migration. Furthermore, 25 DMRs in maternal PBMCs were associated with IgE sensitization to airborne allergens in their children at 5Y, which were functionally annotated to the mTOR (mammalian Target of Rapamycin) signaling pathway. This study supports that DNA methylation is associated with IgE sensitization early in life and revealed new candidate genes for atopy. Moreover, our study provides evidence that maternal DNA methylation levels are associated with IgE sensitization in the child supporting early in utero effects on atopy predisposition.
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Affiliation(s)
- Nathalie Acevedo
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Institute for Immunological Research, University of Cartagena, 130014 Cartagena, Colombia
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, 80138 Napoli, Italy;
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland;
- Institute of Biosciences and Medical Technologies (BioMediTech), Tampere University, 33520 Tampere, Finland
| | - Simon Kebede Merid
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
| | - Paolo Frumento
- Department of Political Sciences, University of Pisa, 56126 Pisa, Italy;
| | - Sören Bruhn
- Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (S.B.); (A.A.)
| | - Anna Andersson
- Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (S.B.); (A.A.)
| | - Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, SE-17121 Solna, Sweden; (C.O.); (E.S.)
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Matteo Bottai
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Gerard H. Koppelman
- Section of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Groningen Research Institute of Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Erik Melén
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Erik Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, SE-17121 Solna, Sweden; (C.O.); (E.S.)
| | - Johan Alm
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (C.S.); (J.K.)
- Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (C.S.); (J.K.)
- Folkhälsan Research Institute, Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland;
- Institute of Biosciences and Medical Technologies (BioMediTech), Tampere University, 33520 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Science for Life Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Correspondence:
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15
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Merid SK, Bustamante M, Standl M, Sunyer J, Heinrich J, Lemonnier N, Aguilar D, Antó JM, Bousquet J, Santa-Marina L, Lertxundi A, Bergström A, Kull I, Wheelock ÅM, Koppelman GH, Melén E, Gruzieva O. Integration of gene expression and DNA methylation identifies epigenetically controlled modules related to PM 2.5 exposure. ENVIRONMENT INTERNATIONAL 2021; 146:106248. [PMID: 33212358 DOI: 10.1016/j.envint.2020.106248] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/24/2020] [Accepted: 10/25/2020] [Indexed: 05/28/2023]
Abstract
Air pollution has been associated with adverse health effects across the life-course. Although underlying mechanisms are unclear, several studies suggested pollutant-induced changes in transcriptomic profiles. In this meta-analysis of transcriptome-wide association studies of 656 children and adolescents from three European cohorts participating in the MeDALL Consortium, we found two differentially expressed transcript clusters (FDR p < 0.05) associated with exposure to particulate matter < 2.5 µm in diameter (PM2.5) at birth, one of them mapping to the MIR1296 gene. Further, by integrating gene expression with DNA methylation using Functional Epigenetic Modules algorithms, we identified 9 and 6 modules in relation to PM2.5 exposure at birth and at current address, respectively (including NR1I2, MAPK6, TAF8 and SCARA3). In conclusion, PM2.5 exposure at birth was linked to differential gene expression in children and adolescents. Importantly, we identified several significant interactome hotspots of gene modules of relevance for complex diseases in relation to PM2.5 exposure.
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Affiliation(s)
- Simon Kebede Merid
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jordi Sunyer
- ISGlobal, Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Ziemssenstraße 1, 80336 Munich, Germany; Allergy and Lung Health Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Nathanaël Lemonnier
- Institute for Advanced Biosciences, UGA-INSERM U1209-CNRS UMR5309, Allée des Alpes, France
| | - Daniel Aguilar
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Barcelona, Spain
| | - Josep Maria Antó
- ISGlobal, Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- Charité, Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany; University Hospital, Montpellier, France; MACVIA-France, Montpellier, France
| | - Loreto Santa-Marina
- Health Research Institute-BIODONOSTIA, Basque Country, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain; Health Department of Basque Government, Sub-directorate of Public Health of Gipuzkoa, 20013 San Sebastian, Spain
| | - Aitana Lertxundi
- Health Research Institute-BIODONOSTIA, Basque Country, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain; Preventive Medicine and Public Health Department, University of Basque Country (UPV/EHU), Spain
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Inger Kull
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs Children's Hospital, Stockholm, Sweden
| | - Åsa M Wheelock
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Erik Melén
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs Children's Hospital, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden.
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16
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Yan S, Chi X, Chang X, Tian M. Analysing the meta-interaction between pathways by gene set topological impact analysis. BMC Genomics 2020; 21:748. [PMID: 33109101 PMCID: PMC7592530 DOI: 10.1186/s12864-020-07148-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pathway analysis is widely applied in transcriptome analysis. Given certain transcriptomic changes, current pathway analysis tools tend to search for the most impacted pathways, which provides insight into underlying biological mechanisms. Further refining of the enriched pathways and extracting functional modules by "crosstalk" analysis have been proposed. However, the upstream/downstream relationships between the modules, which may provide extra biological insights such as the coordination of different functional modules and the signal transduction flow have been ignored. RESULTS To quantitatively analyse the upstream/downstream relationships between functional modules, we developed a novel GEne Set Topological Impact Analysis (GESTIA), which could be used to assemble the enriched pathways and functional modules into a super-module with a topological structure. We showed the advantages of this analysis in the exploration of extra biological insight in addition to the individual enriched pathways and functional modules. CONCLUSIONS GESTIA can be applied to a broad range of pathway/module analysis result. We hope that GESTIA may help researchers to get one additional step closer to understanding the molecular mechanism from the pathway/module analysis results.
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Affiliation(s)
- Shen Yan
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xu Chi
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101300, China
- China National Center for Bioinformation, Chaoyang, Beijing, 101300, China
| | - Xiao Chang
- Department of Dermatology and Venereal Disease, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Mengliang Tian
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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17
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Castresana-Aguirre M, Sonnhammer ELL. Pathway-specific model estimation for improved pathway annotation by network crosstalk. Sci Rep 2020; 10:13585. [PMID: 32788619 PMCID: PMC7423893 DOI: 10.1038/s41598-020-70239-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/06/2020] [Indexed: 12/23/2022] Open
Abstract
Pathway enrichment analysis is the most common approach for understanding which biological processes are affected by altered gene activities under specific conditions. However, it has been challenging to find a method that efficiently avoids false positives while keeping a high sensitivity. We here present a new network-based method ANUBIX based on sampling random gene sets against intact pathway. Benchmarking shows that ANUBIX is considerably more accurate than previous network crosstalk based methods, which have the drawback of modelling pathways as random gene sets. We demonstrate that ANUBIX does not have a bias for finding certain pathways, which previous methods do, and show that ANUBIX finds biologically relevant pathways that are missed by other methods.
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Affiliation(s)
- Miguel Castresana-Aguirre
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden.
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18
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Kim J, Yoon S, Nam D. netGO: R-Shiny package for network-integrated pathway enrichment analysis. Bioinformatics 2020; 36:3283-3285. [DOI: 10.1093/bioinformatics/btaa077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/30/2019] [Accepted: 01/29/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Summary
We present an R-Shiny package, netGO, for novel network-integrated pathway enrichment analysis. The conventional Fisher’s exact test (FET) considers the extent of overlap between target genes and pathway gene-sets, while recent network-based analysis tools consider only network interactions between the two. netGO implements an intuitive framework to integrate both the overlap and networks into a single score, and adaptively resamples genes based on network degrees to assess the pathway enrichment. In benchmark tests for gene expression and genome-wide association study (GWAS) data, netGO captured the relevant gene-sets better than existing tools, especially when analyzing a small number of genes. Specifically, netGO provides user-interactive visualization of the target genes, enriched gene-set and their network interactions for both netGO and FET results for further analysis. For this visualization, we also developed a standalone R-Shiny package shinyCyJS to connect R-shiny and the JavaScript version of cytoscape.
Availability and implementation
netGO R-Shiny package is freely available from github, https://github.com/unistbig/netGO.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Dougu Nam
- School of Life Sciences
- Department of Mathematical Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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19
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Aguilar D, Lemonnier N, Koppelman GH, Melén E, Oliva B, Pinart M, Guerra S, Bousquet J, Anto JM. Understanding allergic multimorbidity within the non-eosinophilic interactome. PLoS One 2019; 14:e0224448. [PMID: 31693680 PMCID: PMC6834334 DOI: 10.1371/journal.pone.0224448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The mechanisms explaining multimorbidity between asthma, dermatitis and rhinitis (allergic multimorbidity) are not well known. We investigated these mechanisms and their specificity in distinct cell types by means of an interactome-based analysis of expression data. METHODS Genes associated to the diseases were identified using data mining approaches, and their multimorbidity mechanisms in distinct cell types were characterized by means of an in silico analysis of the topology of the human interactome. RESULTS We characterized specific pathomechanisms for multimorbidities between asthma, dermatitis and rhinitis for distinct emergent non-eosinophilic cell types. We observed differential roles for cytokine signaling, TLR-mediated signaling and metabolic pathways for multimorbidities across distinct cell types. Furthermore, we also identified individual genes potentially associated to multimorbidity mechanisms. CONCLUSIONS Our results support the existence of differentiated multimorbidity mechanisms between asthma, dermatitis and rhinitis at cell type level, as well as mechanisms common to distinct cell types. These results will help understanding the biology underlying allergic multimorbidity, assisting in the design of new clinical studies.
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MESH Headings
- Asthma/epidemiology
- Asthma/genetics
- Asthma/immunology
- Blood Cells/immunology
- Blood Cells/metabolism
- Cytokines/immunology
- Cytokines/metabolism
- Datasets as Topic
- Dermatitis, Allergic Contact/epidemiology
- Dermatitis, Allergic Contact/genetics
- Dermatitis, Allergic Contact/immunology
- Dermatitis, Atopic/epidemiology
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/immunology
- Gene Expression Profiling
- Humans
- Immunity, Cellular/genetics
- Multimorbidity
- Protein Interaction Maps/genetics
- Protein Interaction Maps/immunology
- Rhinitis, Allergic/epidemiology
- Rhinitis, Allergic/genetics
- Rhinitis, Allergic/immunology
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Affiliation(s)
- Daniel Aguilar
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Barcelona, Spain
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- 6AM Data Mining, Barcelona, Spain
| | - Nathanael Lemonnier
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Gerard H. Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Baldo Oliva
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mariona Pinart
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Stefano Guerra
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Jean Bousquet
- Hopital Arnaud de Villeneuve University Hospital, Montpellier, France
- Charité, Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany
| | - Josep M. Anto
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
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20
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Mora A. Gene set analysis methods for the functional interpretation of non-mRNA data—Genomic range and ncRNA data. Brief Bioinform 2019; 21:1495-1508. [DOI: 10.1093/bib/bbz090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/30/2019] [Accepted: 06/28/2019] [Indexed: 12/31/2022] Open
Abstract
Abstract
Gene set analysis (GSA) is one of the methods of choice for analyzing the results of current omics studies; however, it has been mainly developed to analyze mRNA (microarray, RNA-Seq) data. The following review includes an update regarding general methods and resources for GSA and then emphasizes GSA methods and tools for non-mRNA omics datasets, specifically genomic range data (ChIP-Seq, SNP and methylation) and ncRNA data (miRNAs, lncRNAs and others). In the end, the state of the GSA field for non-mRNA datasets is discussed, and some current challenges and trends are highlighted, especially the use of network approaches to face complexity issues.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health - Chinese Academy of Sciences
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21
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Ogris C, Guala D, Sonnhammer ELL. FunCoup 4: new species, data, and visualization. Nucleic Acids Res 2019; 46:D601-D607. [PMID: 29165593 PMCID: PMC5755233 DOI: 10.1093/nar/gkx1138] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/31/2017] [Indexed: 01/22/2023] Open
Abstract
This release of the FunCoup database (http://funcoup.sbc.su.se) is the fourth generation of one of the most comprehensive databases for genome-wide functional association networks. These functional associations are inferred via integrating various data types using a naive Bayesian algorithm and orthology based information transfer across different species. This approach provides high coverage of the included genomes as well as high quality of inferred interactions. In this update of FunCoup we introduce four new eukaryotic species: Schizosaccharomyces pombe, Plasmodium falciparum, Bos taurus, Oryza sativa and open the database to the prokaryotic domain by including networks for Escherichia coli and Bacillus subtilis. The latter allows us to also introduce a new class of functional association between genes - co-occurrence in the same operon. We also supplemented the existing classes of functional association: metabolic, signaling, complex and physical protein interaction with up-to-date information. In this release we switched to InParanoid v8 as the source of orthology and base for calculation of phylogenetic profiles. While populating all other evidence types with new data we introduce a new evidence type based on quantitative mass spectrometry data. Finally, the new JavaScript based network viewer provides the user an intuitive and responsive platform to further evaluate the results.
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Affiliation(s)
- Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Dimitri Guala
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
| | - Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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22
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Guala D, Ogris C, Müller N, Sonnhammer ELL. Genome-wide functional association networks: background, data & state-of-the-art resources. Brief Bioinform 2019; 21:1224-1237. [PMID: 31281921 PMCID: PMC7373183 DOI: 10.1093/bib/bbz064] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 02/06/2023] Open
Abstract
The vast amount of experimental data from recent advances in the field of high-throughput biology begs for integration into more complex data structures such as genome-wide functional association networks. Such networks have been used for elucidation of the interplay of intra-cellular molecules to make advances ranging from the basic science understanding of evolutionary processes to the more translational field of precision medicine. The allure of the field has resulted in rapid growth of the number of available network resources, each with unique attributes exploitable to answer different biological questions. Unfortunately, the high volume of network resources makes it impossible for the intended user to select an appropriate tool for their particular research question. The aim of this paper is to provide an overview of the underlying data and representative network resources as well as to mention methods of integration, allowing a customized approach to resource selection. Additionally, this report will provide a primer for researchers venturing into the field of network integration.
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Affiliation(s)
- Dimitri Guala
- Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Christoph Ogris
- Computational Cell Maps, Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Nikola Müller
- Computational Cell Maps, Institute of Computational Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Erik L L Sonnhammer
- Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden
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23
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de Anda-Jáuregui G, Guo K, McGregor BA, Feldman EL, Hur J. Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone. BMC SYSTEMS BIOLOGY 2019; 13:1. [PMID: 30616626 PMCID: PMC6322225 DOI: 10.1186/s12918-018-0674-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Aggregation of high-throughput biological data using pathway-based approaches is useful to associate molecular results to functional features related to the studied phenomenon. Biological pathways communicate with one another through the crosstalk phenomenon, forming large networks of interacting processes. RESULTS In this work, we present the pathway crosstalk perturbation network (PXPN) model, a novel model used to analyze and integrate pathway perturbation data based on graph theory. With this model, the changes in activity and communication between pathways observed in transitions between physiological states are represented as networks. The model presented here is agnostic to the type of biological data and pathway definition used and can be implemented to analyze any type of high-throughput perturbation experiments. We present a case study in which we use our proposed model to analyze a gene expression dataset derived from experiments in a BKS-db/db mouse model of type 2 diabetes mellitus-associated neuropathy (DN) and the effects of the drug pioglitazone in this condition. The networks generated describe the profile of pathway perturbation involved in the transitions between the healthy and the pathological state and the pharmacologically treated pathology. We identify changes in the connectivity of perturbed pathways associated to each biological transition, such as rewiring between extracellular matrix, neuronal system, and G-protein coupled receptor signaling pathways. CONCLUSION The PXPN model is a novel, flexible method used to integrate high-throughput data derived from perturbation experiments; it is agnostic to the type of data and enrichment function used, and it is applicable to a wide range of biological phenomena of interest.
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Affiliation(s)
- Guillermo de Anda-Jáuregui
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202 USA
- Present address: Computational Genomics Division, Instituto Nacional de Medicina Genómica, 14610 Ciudad de México, Ciudad de México Mexico
| | - Kai Guo
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202 USA
| | - Brett A. McGregor
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202 USA
| | - Eva L. Feldman
- Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI 48109 USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202 USA
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Jeuken GS, Käll L. A simple null model for inferences from network enrichment analysis. PLoS One 2018; 13:e0206864. [PMID: 30412619 PMCID: PMC6226187 DOI: 10.1371/journal.pone.0206864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/19/2018] [Indexed: 12/31/2022] Open
Abstract
A prevailing technique to infer function from lists of identifications, from molecular biological high-throughput experiments, is over-representation analysis, where the identifications are compared to predefined sets of related genes often referred to as pathways. As at least some pathways are known to be incomplete in their annotation, algorithmic efforts have been made to complement them with information from functional association networks. While the terminology varies in the literature, we will here refer to such methods as Network Enrichment Analysis (NEA). Traditionally, the significance of inferences from NEA has been assigned using a null model constructed from randomizations of the network. Here we instead argue for a null model that more directly relates to the set of genes being studied, and have designed one dynamic programming algorithm that calculates the score distribution of NEA scores that makes it possible to assign unbiased mid p values to inferences. We also implemented a random sampling method, carrying out the same task. We demonstrate that our method obtains a superior statistical calibration as compared to the popular NEA inference engine, BinoX, while also providing statistics that are easier to interpret.
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Affiliation(s)
- Gustavo S. Jeuken
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Box 1031, 17121 Solna, Sweden
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH – Royal Institute of Technology, Box 1031, 17121 Solna, Sweden
- * E-mail:
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25
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Pita-Juárez Y, Altschuler G, Kariotis S, Wei W, Koler K, Green C, Tanzi RE, Hide W. The Pathway Coexpression Network: Revealing pathway relationships. PLoS Comput Biol 2018; 14:e1006042. [PMID: 29554099 PMCID: PMC5875878 DOI: 10.1371/journal.pcbi.1006042] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 03/29/2018] [Accepted: 02/19/2018] [Indexed: 02/02/2023] Open
Abstract
A goal of genomics is to understand the relationships between biological processes. Pathways contribute to functional interplay within biological processes through complex but poorly understood interactions. However, limited functional references for global pathway relationships exist. Pathways from databases such as KEGG and Reactome provide discrete annotations of biological processes. Their relationships are currently either inferred from gene set enrichment within specific experiments, or by simple overlap, linking pathway annotations that have genes in common. Here, we provide a unifying interpretation of functional interaction between pathways by systematically quantifying coexpression between 1,330 canonical pathways from the Molecular Signatures Database (MSigDB) to establish the Pathway Coexpression Network (PCxN). We estimated the correlation between canonical pathways valid in a broad context using a curated collection of 3,207 microarrays from 72 normal human tissues. PCxN accounts for shared genes between annotations to estimate significant correlations between pathways with related functions rather than with similar annotations. We demonstrate that PCxN provides novel insight into mechanisms of complex diseases using an Alzheimer’s Disease (AD) case study. PCxN retrieved pathways significantly correlated with an expert curated AD gene list. These pathways have known associations with AD and were significantly enriched for genes independently associated with AD. As a further step, we show how PCxN complements the results of gene set enrichment methods by revealing relationships between enriched pathways, and by identifying additional highly correlated pathways. PCxN revealed that correlated pathways from an AD expression profiling study include functional clusters involved in cell adhesion and oxidative stress. PCxN provides expanded connections to pathways from the extracellular matrix. PCxN provides a powerful new framework for interrogation of global pathway relationships. Comprehensive exploration of PCxN can be performed at http://pcxn.org/. Genes do not function alone, but interact within pathways to carry out specific biological processes. Pathways, in turn, interact at a higher level to affect major cellular activities such as motility, growth and development. We present a pathway coexpression network (PCxN) that systematically maps and quantifies these high-level interactions and establishes a unifying reference for pathway relationships. The method uses 3,207 human microarrays from 72 normal human tissues and 1,330 of the most well established pathway annotations to describe global relationships between pathways. PCxN accounts for shared genes to estimate correlations between pathways with related functions rather than with redundant pathway definitions. PCxN can be used to discover and explore pathways correlated with a pathway of interest. We applied PCxN to identify key processes related to Alzheimer’s disease (AD), interpreting a mixed genetic association and experimental derived set of disease genes in the context of gene co-expression. We expand the known relationships between pathways identified by gene set enrichment analysis in brain tissues affected with AD. PCxN provides a high-level overview of pathway relationships. PCxN is available as a webtool at http://pcxn.org/, and as a Bioconductor package at http://bioconductor.org/packages/pcxn/.
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Affiliation(s)
- Yered Pita-Juárez
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Gabriel Altschuler
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Sokratis Kariotis
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Wenbin Wei
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Katjuša Koler
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Claire Green
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Winston Hide
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
- National Institute Health Research, Sheffield Biomedical Research Centre, Sheffield, United Kingdom
- * E-mail:
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26
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Connon RE, Jeffries KM, Komoroske LM, Todgham AE, Fangue NA. The utility of transcriptomics in fish conservation. ACTA ACUST UNITED AC 2018; 221:221/2/jeb148833. [PMID: 29378879 DOI: 10.1242/jeb.148833] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.
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Affiliation(s)
- Richard E Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba, Canada R3T 2N2
| | - Lisa M Komoroske
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA.,Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Anne E Todgham
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nann A Fangue
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Detecting pathway relationship in the context of human protein-protein interaction network and its application to Parkinson’s disease. Methods 2017; 131:93-103. [DOI: 10.1016/j.ymeth.2017.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/31/2017] [Accepted: 08/03/2017] [Indexed: 02/06/2023] Open
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