1
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Bhuvaneshwari S, Venkataraman K, Sankaranarayanan K. Exploring potential ion channel targets for rheumatoid arthritis: combination of network analysis and gene expression analysis. Biotechnol Appl Biochem 2024. [PMID: 39049164 DOI: 10.1002/bab.2638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/29/2024] [Indexed: 07/27/2024]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the synovial membrane that leads to the destruction of cartilage and bone. Currently, pharmacological targeting of ion channels is being increasingly recognized as an attractive and feasible strategy for the treatment of RA. The present work employs a network analysis approach to predict the most promising ion channel target for potential RA-treating drugs. A protein-protein interaction map was generated for 343 genes associated with inflammation in RA and ion channel genes using Search Tool for the Retrieval of Interacting Genes and visualized using Cytoscape. Based on the betweenness centrality and traffic values as key topological parameters, 17 hub nodes were identified, including FOS (9800.85), tumor necrosis factor (3654.60), TGFB1 (3305.75), and VEGFA (3052.88). The backbone network constructed with these 17 hub genes was intensely analyzed to identify the most promising ion channel target using network analyzer. Calcium permeating ion channels, especially store-operated calcium entry channels, and their associated regulatory proteins were found to highly interact with RA inflammatory hub genes. This significant ion channel target for RA identified by theoretical and statistical studies was further validated by a pilot case-control gene expression study. Experimental verification of the above findings in 75 RA cases and 25 controls showed increased ORAI1 expression. Thus, with a combination of network analysis approach and gene expression studies, we have explored potential targets for RA treatment.
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Affiliation(s)
- Sampath Bhuvaneshwari
- Ion Channel Biology Laboratory, AU-KBC Research Centre, Madras Institute of Technology, Anna University, Chennai, India
| | | | - Kavitha Sankaranarayanan
- Ion Channel Biology Laboratory, AU-KBC Research Centre, Madras Institute of Technology, Anna University, Chennai, India
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2
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Banik SK, Baishya S, Das Talukdar A, Choudhury MD. Network analysis of atherosclerotic genes elucidates druggable targets. BMC Med Genomics 2022; 15:42. [PMID: 35241081 PMCID: PMC8893053 DOI: 10.1186/s12920-022-01195-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022] Open
Abstract
Background Atherosclerosis is one of the major causes of cardiovascular disease. It is characterized by the accumulation of atherosclerotic plaque in arteries under the influence of inflammatory responses, proliferation of smooth muscle cell, accumulation of modified low density lipoprotein. The pathophysiology of atherosclerosis involves the interplay of a number of genes and metabolic pathways. In traditional translation method, only a limited number of genes and pathways can be studied at once. However, the new paradigm of network medicine can be explored to study the interaction of a large array of genes and their functional partners and their connections with the concerned disease pathogenesis. Thus, in our study we employed a branch of network medicine, gene network analysis as a tool to identify the most crucial genes and the miRNAs that regulate these genes at the post transcriptional level responsible for pathogenesis of atherosclerosis. Result From NCBI database 988 atherosclerotic genes were retrieved. The protein–protein interaction using STRING database resulted in 22,693 PPI interactions among 872 nodes (genes) at different confidence score. The cluster analysis of the 872 genes using MCODE, a plug-in of Cytoscape software revealed a total of 18 clusters, the topological parameter and gene ontology analysis facilitated in the selection of four influential genes viz., AGT, LPL, ITGB2, IRS1 from cluster 3. Further, the miRNAs (miR-26, miR-27, and miR-29 families) targeting these genes were obtained by employing MIENTURNET webtool. Conclusion Gene network analysis assisted in filtering out the 4 probable influential genes and 3 miRNA families in the pathogenesis of atherosclerosis. These genes, miRNAs can be targeted to restrict the occurrence of atherosclerosis. Given the importance of atherosclerosis, any approach in the understanding the genes involved in its pathogenesis can substantially enhance the health care system. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01195-y.
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Affiliation(s)
- Sheuli Kangsa Banik
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Somorita Baishya
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
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3
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Abstract
Drug repositioning is a strategy to identify new uses for existing, approved, or research drugs that are outside the scope of its original medical indication. Drug repurposing is based on the fact that one drug can act on multiple targets or that two diseases can have molecular similarities, among others. Currently, thanks to the rapid advancement of high-performance technologies, a massive amount of biological and biomedical data is being generated. This allows the use of computational methods and models based on biological networks to develop new possibilities for drug repurposing. Therefore, here, we provide an in-depth review of the main applications of drug repositioning that have been carried out using biological network models. The goal of this review is to show the usefulness of these computational methods to predict associations and to find candidate drugs for repositioning in new indications of certain diseases.
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4
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Yin J, Li X, Li F, Lu Y, Zeng S, Zhu F. Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease. Comput Struct Biotechnol J 2021; 19:2318-2328. [PMID: 33995923 PMCID: PMC8105181 DOI: 10.1016/j.csbj.2021.04.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
An appropriate therapeutic index is crucial for drug discovery and development since narrow therapeutic index (NTI) drugs with slight dosage variation may induce severe adverse drug reactions or potential treatment failure. To date, the shared characteristics underlying the targets of NTI drugs have been explored by several studies, which have been applied to identify potential drug targets. However, the association between the drug therapeutic index and the related disease has not been dissected, which is important for revealing the NTI drug mechanism and optimizing drug design. Therefore, in this study, two classes of disease (cancers and cardiovascular disorders) with the largest number of NTI drugs were selected, and the target property of the corresponding NTI drugs was analyzed. By calculating the biological system profiles and human protein–protein interaction (PPI) network properties of drug targets and adopting an AI-based algorithm, differentiated features between two diseases were discovered to reveal the distinct underlying mechanisms of NTI drugs in different diseases. Consequently, ten shared features and four unique features were identified for both diseases to distinguish NTI from NNTI drug targets. These computational discoveries, as well as the newly found features, suggest that in the clinical study of avoiding narrow therapeutic index in those diseases, the ability of target to be a hub and the efficiency of target signaling in the human PPI network should be considered, and it could thus provide novel guidance in the drug discovery and clinical research process and help to estimate the drug safety of cancer and cardiovascular disease.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoxu Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yinjing Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China.,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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5
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Prakash T, Ramachandra NB. Integrated Network and Gene Ontology Analysis Identifies Key Genes and Pathways for Coronary Artery Diseases. Avicenna J Med Biotechnol 2021; 13:15-23. [PMID: 33680369 PMCID: PMC7903433 DOI: 10.18502/ajmb.v13i1.4581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The prevalence of Coronary Artery Disease (CAD) in developing countries is on the rise, owing to rapidly changing lifestyle. Therefore, it is imperative that the underlying genetic and molecular mechanisms be understood to develop specific treatment strategies. Comprehensive disease network and Gene Ontology (GO) studies aid in prioritizing potential candidate genes for CAD and also give insights into gene function by establishing gene and disease pathway relationships. METHODS In the present study, CAD-associated genes were collated from different data sources and protein-protein interaction network was constructed using STRING. Highly interconnected network clusters were inferred and GO analysis was performed. RESULTS Interrelation between genes and pathways were analyzed on ClueGO and 38 candidates were identified from 1475 CAD-associated genes, which were significantly enriched in CAD-related pathways such as metabolism and regulation of lipid molecules, platelet activation, macrophage derived foam cell differentiation, and blood coagulation and fibrin clot formation. DISCUSSION Integrated network and ontology analysis enables biomarker prioritization for common complex diseases such as CAD. Experimental validation and future studies on the prioritized genes may reveal valuable insights into CAD development mechanism and targeted treatment strategies.
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Affiliation(s)
- Tejaswini Prakash
- Genetics and Genomics Lab, Department of Studies in Genetics and Genomics, University of Mysore, Karnataka, India
| | - Nallur B Ramachandra
- Genetics and Genomics Lab, Department of Studies in Genetics and Genomics, University of Mysore, Karnataka, India
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6
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Narmadha D, Pravin A. An intelligent computer-aided approach for target protein prediction in infectious diseases. Soft comput 2020. [DOI: 10.1007/s00500-020-04815-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Rubanova N, Morozova N. Centrality and the shortest path approach in the human interactome. J Bioinform Comput Biol 2019; 17:1950027. [PMID: 31617463 DOI: 10.1142/s0219720019500276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many notions and concepts for network analysis, including the shortest path approach, came to systems biology from the theory of graphs - the field of mathematics that studies graphs. We studied the relationship between the shortest paths and a biologically meaningful molecular path between vertices in human molecular interaction networks. We analyzed the sets of the shortest paths in the human interactome derived from HPRD and HIPPIE databases between all possible combinations of start and end proteins in eight signaling pathways in the KEGG database - NF-kappa B, MAPK, Jak-STAT, mTOR, ErbB, Wnt, TGF-beta, and the signaling part of the apoptotic process. We investigated whether the shortest paths match the canonical paths. We studied whether centrality of vertices and paths in the subnetworks induced by the shortest paths can highlight vertices and paths that are part of meaningful molecular paths. We found that the shortest paths match canonical counterparts only for canonical paths of length 2 or 3 interactions. The shortest paths match longer canonical counterparts with shortcuts or substitutions by protein complex members. We found that high centrality vertices are part of the canonical paths for up to 80% of the canonical paths depending on the database and the length.
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Affiliation(s)
- Natalia Rubanova
- Institut des Hautes Etudes Scientiques, Le Bois-Marie 35 rte de Chartres, Bures-sur-Yvette 91440, France.,Université Paris Diderot, Paris, France.,Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
| | - Nadya Morozova
- Institut des Hautes Etudes Scientiques, Le Bois-Marie 35 rte de Chartres, Bures-sur-Yvette 91440, France.,Plateforme ARN interference (PARi), Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Komarov Botanical Institute, Russian Academy of Sciences (BIN RAS), 197376, Saint Petersburg, Russia
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8
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Saha S, Murmu KC, Biswas M, Chakraborty S, Basu J, Madhulika S, Kolapalli SP, Chauhan S, Sengupta A, Prasad P. Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia. Front Oncol 2019; 9:692. [PMID: 31448224 PMCID: PMC6691814 DOI: 10.3389/fonc.2019.00692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Acute myeloid leukemia (AML) is a common and aggressive hematological malignancy. Acquisition of heterogeneous genetic aberrations and epigenetic dysregulation lead to the transformation of hematopoietic stem cells (HSC) into leukemic stem cells (LSC), which subsequently gives rise to immature blast cells and a leukemic phenotype. LSCs are responsible for disease relapse as current chemotherapeutic regimens are not able to completely eradicate these cellular sub-populations. Therefore, it is critical to improve upon the existing knowledge of LSC specific markers, which would allow for specific targeting of these cells more effectively allowing for their sustained eradication from the cellular milieu. Although significant milestones in decoding the aberrant transcriptional network of various cancers, including leukemia, have been achieved, studies on the involvement of post-transcriptional gene regulation (PTGR) in disease progression are beginning to unfold. RNA binding proteins (RBPs) are key players in mediating PTGR and they regulate the intracellular fate of individual transcripts, from their biogenesis to RNA metabolism, via interactions with RNA binding domains (RBDs). In this study, we have used an integrative approach to systematically profile RBP expression and identify key regulatory RBPs involved in normal myeloid development and AML. We have analyzed RNA-seq datasets (GSE74246) of HSCs, common myeloid progenitors (CMPs), granulocyte-macrophage progenitors (GMPs), monocytes, LSCs, and blasts. We observed that normal and leukemic cells can be distinguished on the basis of RBP expression, which is indicative of their ability to define cellular identity, similar to transcription factors. We identified that distinctly co-expressing modules of RBPs and their subclasses were enriched in hematopoietic stem/progenitor (HSPCs) and differentiated monocytes. We detected expression of DZIP3, an E3 ubiquitin ligase, in HSPCs, knockdown of which promotes monocytic differentiation in cell line model. We identified co-expression modules of RBP genes in LSCs and among these, distinct modules of RBP genes with high and low expression. The expression of several AML-specific RBPs were also validated by quantitative polymerase chain reaction. Network analysis identified densely connected hubs of ribosomal RBP genes (rRBPs) with low expression in LSCs, suggesting the dependency of LSCs on altered ribosome dynamics. In conclusion, our systematic analysis elucidates the RBP transcriptomic landscape in normal and malignant myelopoiesis, and highlights the functional consequences that may result from perturbation of RBP gene expression in these cellular landscapes.
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Affiliation(s)
- Subha Saha
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Krushna Chandra Murmu
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Mayukh Biswas
- Translational Research Unit of Excellence (TRUE), Stem Cell and Leukemia Laboratory, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Sohini Chakraborty
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Jhinuk Basu
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Swati Madhulika
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | | | - Santosh Chauhan
- Cell Biology and Infectious Disease Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Amitava Sengupta
- Translational Research Unit of Excellence (TRUE), Stem Cell and Leukemia Laboratory, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Punit Prasad
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
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9
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Hao T, Wang Q, Zhao L, Wu D, Wang E, Sun J. Analyzing of Molecular Networks for Human Diseases and Drug Discovery. Curr Top Med Chem 2018; 18:1007-1014. [PMID: 30101711 PMCID: PMC6174636 DOI: 10.2174/1568026618666180813143408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 01/11/2023]
Abstract
Molecular networks represent the interactions and relations of genes/proteins, and also encode molecular mechanisms of biological processes, development and diseases. Among the molecular networks, protein-protein Interaction Networks (PINs) have become effective platforms for uncovering the molecular mechanisms of diseases and drug discovery. PINs have been constructed for various organisms and utilized to solve many biological problems. In human, most proteins present their complex functions by interactions with other proteins, and the sum of these interactions represents the human protein interactome. Especially in the research on human disease and drugs, as an emerging tool, the PIN provides a platform to systematically explore the molecular complexities of specific diseases and the references for drug design. In this review, we summarized the commonly used approaches to aid disease research and drug discovery with PINs, including the network topological analysis, identification of novel pathways, drug targets and sub-network biomarkers for diseases. With the development of bioinformatic techniques and biological networks, PINs will play an increasingly important role in human disease research and drug discovery.
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Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Qian Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Lingxuan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Dan Wu
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Edwin Wang
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,University of Calgary Cumming School of Medicine, Calgary, Alberta T2N 4Z6, Canada
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.,Tianjin Bohai Fisheries Research Institute, Tianjin 300221, China
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10
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Ghatge M, Nair J, Sharma A, Vangala RK. Integrative gene ontology and network analysis of coronary artery disease associated genes suggests potential role of ErbB pathway gene EGFR. Mol Med Rep 2018; 17:4253-4264. [PMID: 29328373 PMCID: PMC5802197 DOI: 10.3892/mmr.2018.8393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/14/2017] [Indexed: 12/27/2022] Open
Abstract
Coronary artery disease (CAD) is a major cause of mortality in India, more importantly the young Indians. Combinatorial and integrative approaches to evaluate pathways and genes to gain an improved understanding and potential biomarkers for risk assessment are required. Therefore, 608 genes from the CADgene database version 2.0, classified into 12 functional classes representing the atherosclerotic disease process, were analyzed. Homology analysis of the unique list of gene ontologies (GO) from each functional class gave 8 GO terms represented in 11 and 10 functional classes. Using disease ontology analysis 80 genes belonging to 8 GO terms, using FunDO suggested that 29 of them were identified to be associated with CAD. Extended network analysis of these genes using STRING version 9.1 gave 328 nodes and 4,525 interactions of which the top 5% had a node degree of ≥75 associated with pathways including the ErbB signaling pathway with epidermal growth factor receptor (EGFR) gene as the central hub. Evaluation of EFGR protein levels in age and gender-matched 342 CAD patients vs. 342 control subjects demonstrated significant differences [controls=149.76±2.47 pg/ml and CAD patients stratified into stable angina (SA)=161.65±3.40 pg/ml and myocardial infarction (MI)=171.51±4.26 pg/ml]. Logistic regression analysis suggested that increased EGFR levels exhibit 3-fold higher risk of CAD [odds ratio (OR) 3.51, 95% confidence interval [CI] 1.96–6.28, P≤0.001], upon adjustment for hypertension, diabetes and smoking. A unit increase in EGFR levels increased the risk by 2-fold for SA (OR 2.58, 95% CI 1.25–5.33, P=0.01) and 3.8-fold for MI (OR 3.82, 95% CI 1.94–7.52, P≤0.001) following adjustment. Thus, the use of ontology mapping and network analysis in an integrative manner aids in the prioritization of biomarkers of complex disease.
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Affiliation(s)
- Madankumar Ghatge
- Tata Proteomics and Coagulation Unit, Thrombosis Research Institute, Narayana Hrudayalaya Hospital, Bengaluru, Karnataka 560099, India
| | - Jiny Nair
- Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bengaluru, Karnataka 560099, India
| | - Ankit Sharma
- Manipal University, Manipal, Karnataka 576104, India
| | - Rajani Kanth Vangala
- Tata Proteomics and Coagulation Unit, Thrombosis Research Institute, Narayana Hrudayalaya Hospital, Bengaluru, Karnataka 560099, India
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11
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Grewal N, Singh S, Chand T. Effect of Aggregation Operators on Network-Based Disease Gene Prioritization: A Case Study on Blood Disorders. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:1276-1287. [PMID: 29220322 DOI: 10.1109/tcbb.2016.2599155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Owing to the innate noise in the biological data sources, a single source or a single measure do not suffice for an effective disease gene prioritization. So, the integration of multiple data sources or aggregation of multiple measures is the need of the hour. The aggregation operators combine multiple related data values to a single value such that the combined value has the effect of all the individual values. In this paper, an attempt has been made for applying the fuzzy aggregation on the network-based disease gene prioritization and investigate its effect under noise conditions. This study has been conducted for a set of 15 blood disorders by fusing four different network measures, computed from the protein interaction network, using a selected set of aggregation operators and ranking the genes on the basis of the aggregated value. The aggregation operator-based rankings have been compared with the "Random walk with restart" gene prioritization method. The impact of noise has also been investigated by adding varying proportions of noise to the seed set. The results reveal that for all the selected blood disorders, the Mean of Maximal operator has relatively outperformed the other aggregation operators for noisy as well as non-noisy data.
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12
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Zhang P, Tao L, Zeng X, Qin C, Chen S, Zhu F, Li Z, Jiang Y, Chen W, Chen YZ. A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. Brief Bioinform 2017; 18:1057-1070. [PMID: 27542402 PMCID: PMC5862332 DOI: 10.1093/bib/bbw071] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/14/2016] [Indexed: 02/06/2023] Open
Abstract
The genetic, proteomic, disease and pharmacological studies have generated rich data in protein interaction, disease regulation and drug activities useful for systems-level study of the biological, disease and drug therapeutic processes. These studies are facilitated by the established and the emerging computational methods. More recently, the network descriptors developed in other disciplines have become more increasingly used for studying the protein-protein, gene regulation, metabolic, disease networks. There is an inadequate coverage of these useful network features in the public web servers. We therefore introduced upto 313 literature-reported network descriptors in PROFEAT web server, for describing the topological, connectivity and complexity characteristics of undirected unweighted (uniform binding constants and molecular levels), undirected edge-weighted (varying binding constants), undirected node-weighted (varying molecular levels), undirected edge-node-weighted (varying binding constants and molecular levels) and directed unweighted (oriented process) networks. The usefulness of the PROFEAT computed network descriptors is illustrated by their literature-reported applications in studying the protein-protein, gene regulatory, gene co-expression, protein-drug and metabolic networks. PROFEAT is accessible free of charge at http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi.
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Affiliation(s)
- Peng Zhang
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
- College of Science, Sichuan Agricultural University, Yaan, P. R. China
| | - Lin Tao
- College of Science, Sichuan Agricultural University, Yaan, P. R. China
| | - Xian Zeng
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
| | - Chu Qin
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
| | - Shangying Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
| | - Feng Zhu
- College of Chemistry, Sichuan University, Chengdu, P. R. China
| | - Zerong Li
- Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, P. R. China
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Lab, Shenzhen Technology and Engineering Lab for Personalized Cancer Diagnostics and Therapeutics, and Shenzhen Kivita Innovative Drug Discovery Institute, Tsinghua University Shenzhen Graduate School, Shenzhen, P.R. China
| | - Weiping Chen
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Yu-Zong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore
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13
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Embar V, Handen A, Ganapathiraju MK. Is the average shortest path length of gene set a reflection of their biological relatedness? J Bioinform Comput Biol 2017; 14:1660002. [PMID: 28073302 DOI: 10.1142/s0219720016600027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
When a set of genes are identified to be related to a disease, say through gene expression analysis, it is common to examine the average distance among their protein products in the human interactome as a measure of biological relatedness of these genes. The reasoning for this is that, genes associated with a disease would tend to be functionally related, and that functionally related genes would be closely connected to each other in the interactome. Typically, average shortest path length (ASPL) of disease genes (although referred to as genes in the context of disease-associations, the interactions are among protein-products of these genes) is compared to ASPL of randomly selected genes or to ASPL in a randomly permuted network. We examined whether the ASPL of a set of genes is indeed a good measure of biological relatedness or whether it is simply a characteristic of the degree distribution of those genes. We examined the ASPL of genes sets of some disease and pathway associations and compared them to ASPL of three types of randomly selected control sets: uniform selection, from entire proteome, degree-matched selection, and random permutation of the network. We found that disease associated genes and their degree-matched random genes have comparable ASPL. In other words, ASPL is a characteristic of the degree of the genes and the network topology, and not that of functional coherence.
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Affiliation(s)
- Varsha Embar
- * Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Adam Handen
- † Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15213, USA
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14
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Piroddi M, Albini A, Fabiani R, Giovannelli L, Luceri C, Natella F, Rosignoli P, Rossi T, Taticchi A, Servili M, Galli F. Nutrigenomics of extra-virgin olive oil: A review. Biofactors 2017; 43:17-41. [PMID: 27580701 DOI: 10.1002/biof.1318] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 12/11/2022]
Abstract
Nutrigenomics data on the functional components of olive oil are still sparse, but rapidly increasing. Olive oil is the main source of fat and health-promoting component of the Mediterranean diet. Positive effects have been observed on genes involved in the pathobiology of most prevalent age- and lifestyle-related human conditions, such as cancer, cardiovascular disease and neurodegeneration. Other effects on health-promoting genes have been identified for bioactive components of olives and olive leafs. Omics technologies are offering unique opportunities to identify nutritional and health biomarkers associated with these gene responses, the use of which in personalized and even predictive protocols of investigation, is a main breakthrough in modern medicine and nutrition. Gene regulation properties of the functional components of olive oil, such as oleic acid, biophenols and vitamin E, point to a role for these molecules as natural homeostatic and even hormetic factors with applications as prevention agents in conditions of premature and pathologic aging. Therapeutic applications can be foreseen in conditions of chronic inflammation, and particularly in cancer, which will be discussed in detail in this review paper as major clinical target of nutritional interventions with olive oil and its functional components. © 2016 BioFactors, 43(1):17-41, 2017.
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Affiliation(s)
- Marta Piroddi
- Department of Pharmaceutical Sciences, Nutrition and Clinical Biochemistry Lab, University of Perugia, Italy
| | - Adriana Albini
- IRCCS MultiMedica, Scientific and Technology Pole, Milan, Italy
| | - Roberto Fabiani
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Italy
| | - Lisa Giovannelli
- NEUROFARBA - Section of Phamacology and Toxicology, University of Firenze, Italy
| | - Cristina Luceri
- NEUROFARBA - Section of Phamacology and Toxicology, University of Firenze, Italy
| | - Fausta Natella
- CREA-NUT, Consiglio per La Ricerca in Agricoltura E L'Analisi Dell'Economia Agraria, Food and Nutrition Research Centre, via Ardeatina 546, 00178, Roma, Italy
| | - Patrizia Rosignoli
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Italy
| | - Teresa Rossi
- Research and Statistics, Department, IRCCS "Tecnologie Avanzate E Modelli Assistenziali in Oncologia", Laboratory of Translational Research, Arcispedale S. Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Agnese Taticchi
- Department of Agricultural Food and Environmental Sciences, University of Perugia, Italy
| | - Maurizio Servili
- Department of Agricultural Food and Environmental Sciences, University of Perugia, Italy
| | - Francesco Galli
- Department of Pharmaceutical Sciences, Nutrition and Clinical Biochemistry Lab, University of Perugia, Italy
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15
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Pathania S, Bagler G, Ahuja PS. Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2016; 7:1229. [PMID: 27588023 PMCID: PMC4988974 DOI: 10.3389/fpls.2016.01229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 08/02/2016] [Indexed: 05/07/2023]
Abstract
Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.
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Affiliation(s)
- Shivalika Pathania
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial ResearchPalampur, India
- *Correspondence: Shivalika Pathania
| | - Ganesh Bagler
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial ResearchPalampur, India
- Center for Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi)New Delhi, India
- Centre for Biologically Inspired System Science, Indian Institute of Technology JodhpurJodhpur, India
- Dhirubhai Ambani Institute of Information and Communication TechnologyGandhinagar, India
- Ganesh Bagler
| | - Paramvir S. Ahuja
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial ResearchPalampur, India
- Indian Institute of Science Education and Research (IISER) MohaliMohali, India
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16
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Predicting Abdominal Aortic Aneurysm Target Genes by Level-2 Protein-Protein Interaction. PLoS One 2015; 10:e0140888. [PMID: 26496478 PMCID: PMC4619739 DOI: 10.1371/journal.pone.0140888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/30/2015] [Indexed: 12/22/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is frequently lethal and has no effective pharmaceutical treatment, posing a great threat to human health. Previous bioinformatics studies of the mechanisms underlying AAA relied largely on the detection of direct protein-protein interactions (level-1 PPI) between the products of reported AAA-related genes. Thus, some proteins not suspected to be directly linked to previously reported genes of pivotal importance to AAA might have been missed. In this study, we constructed an indirect protein-protein interaction (level-2 PPI) network based on common interacting proteins encoded by known AAA-related genes and successfully predicted previously unreported AAA-related genes using this network. We used four methods to test and verify the performance of this level-2 PPI network: cross validation, human AAA mRNA chip array comparison, literature mining, and verification in a mouse CaPO4 AAA model. We confirmed that the new level-2 PPI network is superior to the original level-1 PPI network and proved that the top 100 candidate genes predicted by the level-2 PPI network shared similar GO functions and KEGG pathways compared with positive genes.
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17
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Affiliation(s)
- Bai Zhang
- From the Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD (B.Z., Z.Z.); the Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD (Z.Z.); and Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington (Y.T.)
| | - Ye Tian
- From the Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD (B.Z., Z.Z.); the Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD (Z.Z.); and Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington (Y.T.)
| | - Zhen Zhang
- From the Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD (B.Z., Z.Z.); the Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD (Z.Z.); and Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington (Y.T.).
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18
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Nie W, Lv Y, Yan L, Guan T, Li Q, Guo X, Liu W, Feng M, Xu G, Chen X, Lv H. Discovery and characterization of functional modules and pathogenic genes associated with the risk of coronary artery disease. RSC Adv 2015. [DOI: 10.1039/c5ra01920f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An integrated network biology approach for identifying disease risk functional modules and risk pathogenic genes for associated with CAD risk.
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19
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Li ZC, Lai YH, Chen LL, Xie Y, Dai Z, Zou XY. Identifying and prioritizing disease-related genes based on the network topological features. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2214-21. [PMID: 25183318 DOI: 10.1016/j.bbapap.2014.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/22/2014] [Accepted: 08/14/2014] [Indexed: 11/26/2022]
Abstract
Identifying and prioritizing disease-related genes are the most important steps for understanding the pathogenesis and discovering the therapeutic targets. The experimental examination of these genes is very expensive and laborious, and usually has a higher false positive rate. Therefore, it is highly desirable to develop computational methods for the identification and prioritization of disease-related genes. In this study, we develop a powerful method to identify and prioritize candidate disease genes. The novel network topological features with local and global information are proposed and adopted to characterize genes. The performance of these novel features is verified based on the 10-fold cross-validation test and leave-one-out cross-validation test. The proposed features are compared with the published features, and fused strategy is investigated by combining the current features with the published features. And, these combination features are also utilized to identify and prioritize Parkinson's disease-related genes. The results indicate that identified genes are highly related to some molecular process and biological function, which provides new clues for researching pathogenesis of Parkinson's disease. The source code of Matlab is freely available on request from the authors.
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Affiliation(s)
- Zhan-Chao Li
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, People's Republic of China.
| | - Yan-Hua Lai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Li-Li Chen
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Yun Xie
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, People's Republic of China
| | - Zong Dai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Xiao-Yong Zou
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China.
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20
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Nair J, Ghatge M, Kakkar VV, Shanker J. Network analysis of inflammatory genes and their transcriptional regulators in coronary artery disease. PLoS One 2014; 9:e94328. [PMID: 24736319 PMCID: PMC3988072 DOI: 10.1371/journal.pone.0094328] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/15/2014] [Indexed: 01/25/2023] Open
Abstract
Network analysis is a novel method to understand the complex pathogenesis of inflammation-driven atherosclerosis. Using this approach, we attempted to identify key inflammatory genes and their core transcriptional regulators in coronary artery disease (CAD). Initially, we obtained 124 candidate genes associated with inflammation and CAD using Polysearch and CADgene database for which protein-protein interaction network was generated using STRING 9.0 (Search Tool for the Retrieval of Interacting Genes) and visualized using Cytoscape v 2.8.3. Based on betweenness centrality (BC) and node degree as key topological parameters, we identified interleukin-6 (IL-6), vascular endothelial growth factor A (VEGFA), interleukin-1 beta (IL-1B), tumor necrosis factor (TNF) and prostaglandin-endoperoxide synthase 2 (PTGS2) as hub nodes. The backbone network constructed with these five hub genes showed 111 nodes connected via 348 edges, with IL-6 having the largest degree and highest BC. Nuclear factor kappa B1 (NFKB1), signal transducer and activator of transcription 3 (STAT3) and JUN were identified as the three core transcription factors from the regulatory network derived using MatInspector. For the purpose of validation of the hub genes, 97 test networks were constructed, which revealed the accuracy of the backbone network to be 0.7763 while the frequency of the hub nodes remained largely unaltered. Pathway enrichment analysis with ClueGO, KEGG and REACTOME showed significant enrichment of six validated CAD pathways - smooth muscle cell proliferation, acute-phase response, calcidiol 1-monooxygenase activity, toll-like receptor signaling, NOD-like receptor signaling and adipocytokine signaling pathways. Experimental verification of the above findings in 64 cases and 64 controls showed increased expression of the five candidate genes and the three transcription factors in the cases relative to the controls (p<0.05). Thus, analysis of complex networks aid in the prioritization of genes and their transcriptional regulators in complex diseases.
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Affiliation(s)
- Jiny Nair
- Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bengaluru, Karnataka, India
| | - Madankumar Ghatge
- Tata Proteomics and Coagulation Unit, Thrombosis Research Unit, Bengaluru, Karnataka, India
| | - Vijay V. Kakkar
- Thrombosis Research Institute, Bengaluru, Karnataka, India
- Thrombosis Research Institute, London, United Kingdom
| | - Jayashree Shanker
- Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bengaluru, Karnataka, India
- * E-mail:
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21
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Survey of network-based approaches to research of cardiovascular diseases. BIOMED RESEARCH INTERNATIONAL 2014; 2014:527029. [PMID: 24772427 PMCID: PMC3977459 DOI: 10.1155/2014/527029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/07/2014] [Indexed: 01/08/2023]
Abstract
Cardiovascular diseases (CVDs) are the leading health problem worldwide. Investigating causes and mechanisms of CVDs calls for an integrative approach that would take into account its complex etiology. Biological networks generated from available data on biomolecular interactions are an excellent platform for understanding interconnectedness of all processes within a living cell, including processes that underlie diseases. Consequently, topology of biological networks has successfully been used for identifying genes, pathways, and modules that govern molecular actions underlying various complex diseases. Here, we review approaches that explore and use relationships between topological properties of biological networks and mechanisms underlying CVDs.
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22
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Safari-Alighiarloo N, Taghizadeh M, Rezaei-Tavirani M, Goliaei B, Peyvandi AA. Protein-protein interaction networks (PPI) and complex diseases. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2014; 7:17-31. [PMID: 25436094 PMCID: PMC4017556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 12/23/2013] [Indexed: 11/16/2022]
Abstract
The physical interaction of proteins which lead to compiling them into large densely connected networks is a noticeable subject to investigation. Protein interaction networks are useful because of making basic scientific abstraction and improving biological and biomedical applications. Based on principle roles of proteins in biological function, their interactions determine molecular and cellular mechanisms, which control healthy and diseased states in organisms. Therefore, such networks facilitate the understanding of pathogenic (and physiologic) mechanisms that trigger the onset and progression of diseases. Consequently, this knowledge can be translated into effective diagnostic and therapeutic strategies. Furthermore, the results of several studies have proved that the structure and dynamics of protein networks are disturbed in complex diseases such as cancer and autoimmune disorders. Based on such relationship, a novel paradigm is suggested in order to confirm that the protein interaction networks can be the target of therapy for treatment of complex multi-genic diseases rather than individual molecules with disrespect the network.
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Affiliation(s)
- Nahid Safari-Alighiarloo
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghizadeh
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Tehran University, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Goliaei
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Tehran University, Tehran, Iran
| | - Ali Asghar Peyvandi
- Hearing Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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23
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A network study of chinese medicine xuesaitong injection to elucidate a complex mode of action with multicompound, multitarget, and multipathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 2013:652373. [PMID: 24058375 PMCID: PMC3766588 DOI: 10.1155/2013/652373] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 07/10/2013] [Indexed: 12/23/2022]
Abstract
Chinese medicine has evolved from thousands of years of empirical applications and experiences of combating diseases. It has become widely recognized that the Chinese medicine acts through complex mechanisms featured as multicompound, multitarget and multipathway. However, there is still a lack of systematic experimental studies to elucidate the mechanisms of Chinese medicine. In this study, the differentially expressed genes (DEGs) were identified from myocardial infarction rat model treated with Xuesaitong Injection (XST), a Chinese medicine consisting of the total saponins from Panax notoginseng (Burk.) F. H. Chen (Chinese Sanqi). A network-based approach was developed to combine DEGs related to cardiovascular diseases (CVD) with lines of evidence from the literature mining to investigate the mechanism of action (MOA) of XST on antimyocardial infarction. A compound-target-pathway network of XST was constructed by connecting compounds to DEGs validated with literature lines of evidence and the pathways that are functionally enriched. Seventy potential targets of XST were identified in this study, of which 32 were experimentally validated either by our in vitro assays or by CVD-related literatures. This study provided for the first time a network view on the complex MOA of antimyocardial infarction through multiple targets and pathways.
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24
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Sarajlić A, Janjić V, Stojković N, Radak D, Pržulj N. Network topology reveals key cardiovascular disease genes. PLoS One 2013; 8:e71537. [PMID: 23977067 PMCID: PMC3744556 DOI: 10.1371/journal.pone.0071537] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/29/2013] [Indexed: 11/19/2022] Open
Abstract
The structure of protein-protein interaction (PPI) networks has already been successfully used as a source of new biological information. Even though cardiovascular diseases (CVDs) are a major global cause of death, many CVD genes still await discovery. We explore ways to utilize the structure of the human PPI network to find important genes for CVDs that should be targeted by drugs. The hope is to use the properties of such important genes to predict new ones, which would in turn improve a choice of therapy. We propose a methodology that examines the PPI network wiring around genes involved in CVDs. We use the methodology to identify a subset of CVD-related genes that are statistically significantly enriched in drug targets and "driver genes." We seek such genes, since driver genes have been proposed to drive onset and progression of a disease. Our identified subset of CVD genes has a large overlap with the Core Diseasome, which has been postulated to be the key to disease formation and hence should be the primary object of therapeutic intervention. This indicates that our methodology identifies "key" genes responsible for CVDs. Thus, we use it to predict new CVD genes and we validate over 70% of our predictions in the literature. Finally, we show that our predicted genes are functionally similar to currently known CVD drug targets, which confirms a potential utility of our methodology towards improving therapy for CVDs.
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Affiliation(s)
- Anida Sarajlić
- Department of Computing, Imperial College London, London, United Kingdom
| | - Vuk Janjić
- Department of Computing, Imperial College London, London, United Kingdom
| | - Neda Stojković
- Institute for Cardiovascular Disease “Dedinje,” University of Belgrade, Belgrade, Serbia
| | - Djordje Radak
- Institute for Cardiovascular Disease “Dedinje,” University of Belgrade, Belgrade, Serbia
| | - Nataša Pržulj
- Department of Computing, Imperial College London, London, United Kingdom
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25
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Konstantinidou V, Covas MI, Sola R, Fitó M. Up-to date knowledge on the in vivo transcriptomic effect of the Mediterranean diet in humans. Mol Nutr Food Res 2013; 57:772-83. [DOI: 10.1002/mnfr.201200613] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/12/2012] [Accepted: 12/15/2012] [Indexed: 01/17/2023]
Affiliation(s)
- Valentini Konstantinidou
- Research Unit on Lipids and Atherosclerosis, Hospital Universitari Sant Joan, IISPV; Universitat Rovira i Virgili and CIBER Diabetes and Associated Metabolic Disorders; (CIBERDEM); Reus; Spain
| | - Maria-Isabel Covas
- Cardiovascular Risk and Nutrition Research Group; Mar Institute of Medical Research (IMIM), CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN); Barcelona; Spain
| | - Rosa Sola
- Research Unit on Lipids and Atherosclerosis, Hospital Universitari Sant Joan, IISPV; Universitat Rovira i Virgili and CIBER Diabetes and Associated Metabolic Disorders; (CIBERDEM); Reus; Spain
| | - Montserrat Fitó
- Cardiovascular Risk and Nutrition Research Group; Mar Institute of Medical Research (IMIM), CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN); Barcelona; Spain
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