201
|
Choudhury AD, Chowdhury AS. CHANGE: Cardiac Health Analysis Using Graph Eigenvalues. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018; 2018:4025-4029. [PMID: 30441240 DOI: 10.1109/embc.2018.8513302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Coronary Artery Disease (CAD) is an important problem in cardiac health and is a leading cause of human mortality. Prior arts have shown that features extracted from non-invasive Photoplethysmogram (PPG) signal are effective in classifying CAD. In this paper, we represent cardiac health as a graph (CHG) in order to exploit the dependencies of PPG features as well as the metadata features. We then compute spectral features from the eigenvalues of the graph Laplacian of CHG. Finally, k-means algorithm is employed for classifying the data into CAD and non-CAD. Unsupervised experiments on a cohort with 32 participants yields 88% accuracy and demonstrates advantage of the proposed formulation over a baseline and two state-of-the-art approaches.
Collapse
|
202
|
Lindfors E, van Dam JCJ, Lam CMC, Zondervan NA, Martins dos Santos VAP, Suarez-Diez M. SyNDI: synchronous network data integration framework. BMC Bioinformatics 2018; 19:403. [PMID: 30400817 PMCID: PMC6219086 DOI: 10.1186/s12859-018-2426-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/10/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way to model these systems with the idea of representing biomolecules as nodes and their interactions as edges. Very often the input data come from various sorts of omics analyses. Those resulting networks sometimes describe a wide range of aspects, for example different experiment conditions, species, tissue types, stimulating factors, mutants, or simply distinct interaction features of the same network produced by different algorithms. For these scenarios, synchronous visualization of more than one distinct network is an excellent mean to explore all the relevant networks efficiently. In addition, complementary analysis methods are needed and they should work in a workflow manner in order to gain maximal biological insights. RESULTS In order to address the aforementioned needs, we have developed a Synchronous Network Data Integration (SyNDI) framework. This framework contains SyncVis, a Cytoscape application for user-friendly synchronous and simultaneous visualization of multiple biological networks, and it is seamlessly integrated with other bioinformatics tools via the Galaxy platform. We demonstrated the functionality and usability of the framework with three biological examples - we analyzed the distinct connectivity of plasma metabolites in networks associated with high or low latent cardiovascular disease risk; deeper insights were obtained from a few similar inflammatory response pathways in Staphylococcus aureus infection common to human and mouse; and regulatory motifs which have not been reported associated with transcriptional adaptations of Mycobacterium tuberculosis were identified. CONCLUSIONS Our SyNDI framework couples synchronous network visualization seamlessly with additional bioinformatics tools. The user can easily tailor the framework for his/her needs by adding new tools and datasets to the Galaxy platform.
Collapse
Affiliation(s)
- Erno Lindfors
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany
| | - Jesse C. J. van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - Niels A. Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A. P. Martins dos Santos
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|
203
|
Bush SJ, Powell-Smith A, Freeman TC. Network analysis of the social and demographic influences on name choice within the UK (1838-2016). PLoS One 2018; 13:e0205759. [PMID: 30379928 PMCID: PMC6209202 DOI: 10.1371/journal.pone.0205759] [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: 06/18/2018] [Accepted: 10/01/2018] [Indexed: 11/21/2022] Open
Abstract
Chosen names reflect changes in societal values, personal tastes and cultural diversity. Vogues in name usage can be easily shown on a case by case basis, by plotting the rise and fall in their popularity over time. However, individual name choices are not made in isolation and trends in naming are better understood as group-level phenomena. Here we use network analysis to examine onomastic (name) datasets in order to explore the influences on name choices within the UK over the last 170 years. Using a large representative sample of approximately 22 million forenames from England and Wales given between 1838 and 2014, along with a complete population sample of births registered between 1996 and 2016, we demonstrate how trends in name usage can be visualised as network graphs. By exploring the structure of these graphs various patterns of name use become apparent, a consequence of external social forces, such as migration, operating in concert with internal mechanisms of change. In general, we show that the topology of network graphs can reveal naming vogues, and that naming vogues in part reflect social and demographic changes. Many name choices are consistent with a self-correcting feedback loop, whereby rarer names become common because there are virtues perceived in their rarity, yet with these perceived virtues lost upon increasing commonality. Towards the present day, we can speculate that the comparatively greater range of media, freedom of movement, and ability to maintain globally-distributed social networks increases the number of possible names, but also ensures they may more quickly be perceived as commonplace. Consequently, contemporary naming vogues are relatively short-lived with many name choices appearing a balance struck between recognisability and rarity. The data are available in multiple forms including via an easy-to-use web interface at http://demos.flourish.studio/namehistory.
Collapse
Affiliation(s)
- Stephen J. Bush
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- * E-mail:
| | | | - Tom C. Freeman
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| |
Collapse
|
204
|
Singh A, Rawlings CJ, Hassani-Pak K. KnetMaps: a BioJS component to visualize biological knowledge networks. F1000Res 2018; 7:1651. [PMID: 30755790 PMCID: PMC6347035 DOI: 10.12688/f1000research.16605.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
KnetMaps is a
BioJS component for the interactive visualization of biological knowledge networks. It is well suited for applications that need to visualise complementary, connected and content-rich data in a single view in order to help users to traverse pathways linking entities of interest, for example to go from genotype to phenotype. KnetMaps loads data in JSON format, visualizes the structure and content of knowledge networks using lightweight JavaScript libraries, and supports interactive touch gestures. KnetMaps uses effective visualization techniques to prevent information overload and to allow researchers to progressively build their knowledge.
Collapse
Affiliation(s)
- Ajit Singh
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | - Keywan Hassani-Pak
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| |
Collapse
|
205
|
Mortezaei Z, Cazier JB, Mehrabi AA, Cheng C, Masoudi-Nejad A. Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis. J Cell Biochem 2018; 120:5459-5471. [PMID: 30302804 DOI: 10.1002/jcb.27825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
Understanding the genetic causes of neurodegenerative disease (ND) can be useful for their prevention and treatment. Among the genetic variations responsible for ND, heritable germline variants have been discovered in genome-wide association studies (GWAS), and nonheritable somatic mutations have been discovered in sequencing projects. Distinguishing the important initiating genes in ND and comparing the importance of heritable and nonheritable genetic variants for treating ND are important challenges. In this study, we analysed GWAS results, somatic mutations and drug targets of ND from large databanks by performing directed network-based analysis considering a randomised network hypothesis testing procedure. A disease-associated biological network was created in the context of the functional interactome, and the nonrandom topological characteristics of directed-edge classes were interpreted. Hierarchical network analysis indicated that drug targets tend to lie upstream of somatic mutations and germline variants. Furthermore, using directed path length information and biological explanations, we provide information on the most important genes in these created node classes and their associated drugs. Finally, we identified nine germline variants overlapping with drug targets for ND, seven somatic mutations close to drug targets from the hierarchical network analysis and six crucial genes in controlling other genes from the network analysis. Based on these findings, some drugs have been proposed for treating ND via drug repurposing. Our results provide new insights into the therapeutic actionability of GWAS results and somatic mutations for ND. The interesting properties of each node class and the existing relationships between them can broaden our knowledge of ND.
Collapse
Affiliation(s)
- Zahra Mortezaei
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Jean-Baptiste Cazier
- Centre for Computational Biology, Haworth Building, University of Birmingham, Birmingham, UK
| | - Ali Ashraf Mehrabi
- Department of Biometry and Plant Genetics, University of Ilam, Ilam, Iran
| | - Chao Cheng
- Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| |
Collapse
|
206
|
Kuntal BK, Chandrakar P, Sadhu S, Mande SS. 'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets. ISME JOURNAL 2018; 13:442-454. [PMID: 30287886 DOI: 10.1038/s41396-018-0291-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/05/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.
Collapse
Affiliation(s)
- Bhusan K Kuntal
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Pune, 411 008, India
| | - Pranjal Chandrakar
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.,Decision Sciences, Indian Institute of Management Bangalore, Bannerghatta Road, Bengaluru, Karnataka, 560076, India
| | - Sudipta Sadhu
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.
| |
Collapse
|
207
|
Lázaro-Guevara J, Flores-Robles B, Garrido K, Pinillos-Aransay V, Elena-Ibáñez A, Merino-Meléndez L, López-Martínez J, Victoriano-Lacalle R. Gene's hubs in retinal diseases: A retinal disease network. Heliyon 2018; 4:e00867. [PMID: 30417144 PMCID: PMC6218668 DOI: 10.1016/j.heliyon.2018.e00867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/28/2018] [Accepted: 10/11/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Retinal diseases associated with the dysfunction or death of photoreceptors are a major cause of blindness around the world, improvements in genetics tools, like next generation sequencing (NGS) allows the discovery of genes and genetic changes that lead to many of those retinal diseases. Though, there very few databases that explores a wide spectrum of retinal diseases, phenotypes, genes, and proteins, thus creating the need for a more comprehensive database, that groups all these parameters. METHODS Multiple open access databases were compiled into a new comprehensive database. A biological network was then crated, and organized using Cytoscape. The network was scrutinized for presence of hubs, measuring the concentration of grouped nodes. Finally, a trace back analysis was performed in areas were the power law reports a high r-squared value near one, that indicates high nodes density. RESULTS This work leads to creation of a retinal database that includes 324 diseases, 803 genes, 463 phenotypes, and 2461 proteins. Four biological networks (1) a disease and gene network connected by common phenotypes, (2) a disease and phenotype network connected by common genes, (3) a disease and gene network with shared disease or gene as the cause of an edge, and (4) a protein and disease network. The resulting networks will allow users to have easier searching for retinal diseases, phenotypes, genes, and proteins and their interrelationships. CONCLUSIONS These networks have a broader range of information than previously available ones, helping clinicians in the comprehension of this complex group of diseases.
Collapse
Affiliation(s)
| | | | - K. Garrido
- Paediatrics Department Guatemalan Social Secure Guatemala, Guatemala
| | | | | | | | | | | |
Collapse
|
208
|
Donovan EL, Lopes EBP, Batushansky A, Kinter M, Griffin TM. Independent effects of dietary fat and sucrose content on chondrocyte metabolism and osteoarthritis pathology in mice. Dis Model Mech 2018; 11:dmm.034827. [PMID: 30018076 PMCID: PMC6176996 DOI: 10.1242/dmm.034827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/09/2018] [Indexed: 12/11/2022] Open
Abstract
Obesity is one of the most significant risk factors for knee osteoarthritis. However, therapeutic strategies to prevent or treat obesity-associated osteoarthritis are limited because of uncertainty about the etiology of disease, particularly with regard to metabolic factors. High-fat-diet-induced obese mice have become a widely used model for testing hypotheses about how obesity increases the risk of osteoarthritis, but progress has been limited by variation in disease severity, with some reports concluding that dietary treatment alone is insufficient to induce osteoarthritis in mice. We hypothesized that increased sucrose content of typical low-fat control diets contributes to osteoarthritis pathology and thus alters outcomes when evaluating the effects of a high-fat diet. We tested this hypothesis in male C57BL/6J mice by comparing the effects of purified diets that independently varied sucrose or fat content from 6 to 26 weeks of age. Outcomes included osteoarthritis pathology, serum metabolites, and cartilage gene and protein changes associated with cellular metabolism and stress-response pathways. We found that the relative content of sucrose versus cornstarch in low-fat iso-caloric purified diets caused substantial differences in serum metabolites, joint pathology, and cartilage metabolic and stress-response pathways, despite no differences in body mass or body fat. We also found that higher dietary fat increased fatty acid metabolic enzymes in cartilage. The findings indicate that the choice of control diets should be carefully considered in mouse osteoarthritis studies. Our study also indicates that altered cartilage metabolism might be a contributing factor to how diet and obesity increase the risk of osteoarthritis. Summary: The contribution of metabolic factors to obesity-associated knee osteoarthritis is uncertain. Here, we show how dietary fat and sucrose independently alter cartilage metabolic enzymes and osteoarthritis pathophysiology in mice.
Collapse
Affiliation(s)
- Elise L Donovan
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, OK 73104, USA
| | - Erika Barboza Prado Lopes
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, OK 73104, USA
| | - Albert Batushansky
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, OK 73104, USA
| | - Mike Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, OK 73104, USA.,Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Timothy M Griffin
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, OK 73104, USA .,Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Department of Biochemistry and Molecular Biology and Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| |
Collapse
|
209
|
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. BMC Genomics 2018; 19:594. [PMID: 30086717 PMCID: PMC6081845 DOI: 10.1186/s12864-018-4972-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/31/2018] [Indexed: 12/20/2022] Open
Abstract
Background The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues. Results Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development. Conclusion Expression profiles obtained from public RNA-seq datasets – despite being generated by different laboratories using different methodologies – can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4972-7) contains supplementary material, which is available to authorized users.
Collapse
|
210
|
Pawar S, Ashraf MI, Mujawar S, Mishra R, Lahiri C. In silico Identification of the Indispensable Quorum Sensing Proteins of Multidrug Resistant Proteus mirabilis. Front Cell Infect Microbiol 2018; 8:269. [PMID: 30131943 PMCID: PMC6090301 DOI: 10.3389/fcimb.2018.00269] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/17/2018] [Indexed: 11/13/2022] Open
Abstract
Catheter-associated urinary tract infections (CAUTI) is an alarming hospital based disease with the increase of multidrug resistance (MDR) strains of Proteus mirabilis. Cases of long term hospitalized patients with multiple episodes of antibiotic treatments along with urinary tract obstruction and/or undergoing catheterization have been reported to be associated with CAUTI. The cases are complicated due to the opportunist approach of the pathogen having robust swimming and swarming capability. The latter giving rise to biofilms and probably inducible through autoinducers make the scenario quite complex. High prevalence of long-term hospital based CAUTI for patients along with moderate percentage of morbidity, cropping from ignorance about drug usage and failure to cure due to MDR, necessitates an immediate intervention strategy effective enough to combat the deadly disease. Several reports and reviews focus on revealing the important genes and proteins, essential to tackle CAUTI caused by P. mirabilis. Despite longitudinal countrywide studies and methodical strategies to circumvent the issues, effective means of unearthing the most indispensable proteins to target for therapeutic uses have been meager. Here, we report a strategic approach for identifying the most indispensable proteins from the genome of P. mirabilis strain HI4320, besides comparing the interactomes comprising the autoinducer-2 (AI-2) biosynthetic pathway along with other proteins involved in biofilm formation and responsible for virulence. Essentially, we have adopted a theoretical network model based approach to construct a set of small protein interaction networks (SPINs) along with the whole genome (GPIN) to computationally identify the crucial proteins involved in the phenomenon of quorum sensing (QS) and biofilm formation and thus, could be therapeutically targeted to fight out the MDR threats to antibiotics of P. mirabilis. Our approach utilizes the functional modularity coupled with k-core analysis and centrality scores of eigenvector as a measure to address the pressing issues.
Collapse
Affiliation(s)
- Shrikant Pawar
- Department of Computer Science, Georgia State University, Atlanta, GA, United States.,Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Md Izhar Ashraf
- Department of Computer Applications, B.S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India.,Theoretical Physics, The Institute of Mathematical Sciences, Chennai, India
| | - Shama Mujawar
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Rohit Mishra
- Department of Bioinformatics, G.N. Khalsa College, University of Mumbai, Mumbai, India
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| |
Collapse
|
211
|
Shukla A, Dahiya S, Onteru SK, Singh D. Differentially expressed miRNA-210 during follicular-luteal transition regulates pre-ovulatory granulosa cell function targeting HRas and EFNA3. J Cell Biochem 2018; 119:7934-7943. [PMID: 29131373 DOI: 10.1002/jcb.26508] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/09/2017] [Indexed: 01/19/2023]
Abstract
Ovarian folliculogenesis, ovulation, and luteinization are an important prerequisite for fertility performance in mammals. Spatial and temporal key factors and proteins for their regulation are well known. Recent advancement in the field of molecular biology led to the discovery of another class of gene regulators, microRNA (miRNA). Previous studies on profiling of miRNA in buffalo ovaries revealed that miRNA-210 (miR-210) is differently expressed in follicular-luteal transition. Therefore, the present study was planned to ascertain the role of miR-210 in buffalo granulosa cells. Cultured granulosa cells were transfected with miR-210 mimic. Effect of overexpression of miR-210 was analyzed on granulosa cell marker genes (CYP19A1 and PCNA) which were significantly downregulated (P < 0.05). Further, target genes of miR-210 were screened using Target Scan software v7.1 and a list of 37 genes with cumulative weight context score (CWCS) > 0.5 was sorted followed by their functional annotation and network analyses using PANTHER and STRING software. Bioinformatics analyses identified HRas gene as a potential hub gene of miR-210 targeted genes. HRas has been shown to be involved in diverse biological pathways regulating ovarian functions. An expression analysis of HRas was further validated both in vitro and in vivo. EFNA3 (EFHRIN-A3), another identified target of miR-210 known to be involved in angiogenesis, was also downregulated in miR-210 transfected granulosa cells. In conclusion, the present study demonstrated that miR-210 can regulate granulosa cell function at preovulatory stage through HRas and EFNA3. Further studies are needed to find the mechanism how miR-210 regulates the granulosa cells function through these targets.
Collapse
Affiliation(s)
- Astha Shukla
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Sunita Dahiya
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Suneel K Onteru
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Dheer Singh
- Molecular Endocrinology, Functional Genomics and Systems Biology Laboratory, Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| |
Collapse
|
212
|
Structure Optimization for Large Gene Networks Based on Greedy Strategy. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2018; 2018:9674108. [PMID: 30013615 PMCID: PMC6022335 DOI: 10.1155/2018/9674108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023]
Abstract
In the last few years, gene networks have become one of most important tools to model biological processes. Among other utilities, these networks visually show biological relationships between genes. However, due to the large amount of the currently generated genetic data, their size has grown to the point of being unmanageable. To solve this problem, it is possible to use computational approaches, such as heuristics-based methods, to analyze and optimize gene network's structure by pruning irrelevant relationships. In this paper we present a new method, called GeSOp, to optimize large gene network structures. The method is able to perform a considerably prune of the irrelevant relationships comprising the input network. To do so, the method is based on a greedy heuristic to obtain the most relevant subnetwork. The performance of our method was tested by means of two experiments on gene networks obtained from different organisms. The first experiment shows how GeSOp is able not only to carry out a significant reduction in the size of the network, but also to maintain the biological information ratio. In the second experiment, the ability to improve the biological indicators of the network is checked. Hence, the results presented show that GeSOp is a reliable method to optimize and improve the structure of large gene networks.
Collapse
|
213
|
Abstract
BACKGROUND Systems biology is an important field for understanding whole biological mechanisms composed of interactions between biological components. One approach for understanding complex and diverse mechanisms is to analyze biological pathways. However, because these pathways consist of important interactions and information on these interactions is disseminated in a large number of biomedical reports, text-mining techniques are essential for extracting these relationships automatically. RESULTS In this study, we applied node2vec, an algorithmic framework for feature learning in networks, for relationship extraction. To this end, we extracted genes from paper abstracts using pkde4j, a text-mining tool for detecting entities and relationships. Using the extracted genes, a co-occurrence network was constructed and node2vec was used with the network to generate a latent representation. To demonstrate the efficacy of node2vec in extracting relationships between genes, performance was evaluated for gene-gene interactions involved in a type 2 diabetes pathway. Moreover, we compared the results of node2vec to those of baseline methods such as co-occurrence and DeepWalk. CONCLUSIONS Node2vec outperformed existing methods in detecting relationships in the type 2 diabetes pathway, demonstrating that this method is appropriate for capturing the relatedness between pairs of biological entities involved in biological pathways. The results demonstrated that node2vec is useful for automatic pathway construction.
Collapse
Affiliation(s)
- Munui Kim
- Department of Library and Information Science, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Seung Han Baek
- Department of Library and Information Science, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Min Song
- Department of Library and Information Science, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea.
| |
Collapse
|
214
|
Martínez O, Reyes-Valdés MH. On an algorithmic definition for the components of the minimal cell. PLoS One 2018; 13:e0198222. [PMID: 29856803 PMCID: PMC5983409 DOI: 10.1371/journal.pone.0198222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/15/2018] [Indexed: 11/19/2022] Open
Abstract
Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell components and thus define the ‘minimal cell’ and the corresponding ‘minimal genome’, we postulate that the synthesis of all cell elements can be represented as a finite set of binary operators, and within this framework we show that cell elements that depend on their previous existence to be synthesized are those that are essential for cell survival. An algorithm to distinguish essential cell elements is presented and demonstrated within an interactome. Data and functions implementing the algorithm are given as supporting information. We expect that this algorithmic approach will lead to the determination of the complete interactome of the minimal cell, which could then be experimentally validated. The assumptions behind this hypothesis as well as its consequences for experimental and theoretical biology are discussed.
Collapse
Affiliation(s)
- Octavio Martínez
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
- * E-mail:
| | - M. Humberto Reyes-Valdés
- Graduate Program on Plant Genetic Resources for Arid Lands, Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila, México
| |
Collapse
|
215
|
Villeneuve DL, Angrish MM, Fortin MC, Katsiadaki I, Leonard M, Margiotta-Casaluci L, Munn S, O’Brien JM, Pollesch NL, Smith LC, Zhang X, Knapen D. Adverse outcome pathway networks II: Network analytics. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2018; 37:1734-1748. [PMID: 29492998 PMCID: PMC6010347 DOI: 10.1002/etc.4124] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/11/2017] [Accepted: 02/24/2018] [Indexed: 05/20/2023]
Abstract
Toxicological responses to stressors are more complex than the simple one-biological-perturbation to one-adverse-outcome model portrayed by individual adverse outcome pathways (AOPs). Consequently, the AOP framework was designed to facilitate de facto development of AOP networks that can aid in the understanding and prediction of pleiotropic and interactive effects more common to environmentally realistic, complex exposure scenarios. The present study introduces nascent concepts related to the qualitative analysis of AOP networks. First, graph theory-based approaches for identifying important topological features are illustrated using 2 example AOP networks derived from existing AOP descriptions. Second, considerations for identifying the most significant path(s) through an AOP network from either a biological or risk assessment perspective are described. Finally, approaches for identifying interactions among AOPs that may result in additive, synergistic, or antagonistic responses (or previously undefined emergent patterns of response) are introduced. Along with a companion article (part I), these concepts set the stage for the development of tools and case studies that will facilitate more rigorous analysis of AOP networks, and the utility of AOP network-based predictions, for use in research and regulatory decision-making. The present study addresses one of the major themes identified through a Society of Environmental Toxicology and Chemistry Horizon Scanning effort focused on advancing the AOP framework. Environ Toxicol Chem 2018;37:1734-1748. © 2018 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Collapse
Affiliation(s)
- Daniel L. Villeneuve
- United States Environmental Protection Agency, Mid-Continent Ecology Division, Duluth, MN, USA
| | - Michelle M. Angrish
- United States Environmental Protection Agency, National Center for Environmental Assessment, Research Triangle Park, NC, USA
| | - Marie C. Fortin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA
| | - Ioanna Katsiadaki
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Marc Leonard
- L’Oréal Advanced Research, Aulnay-sous-Bois, France
| | - Luigi Margiotta-Casaluci
- Institute of Environment, Health and Societies, Brunel University London, London, United Kingdom
| | - Sharon Munn
- Joint Research Centre (JRC), European Commission, Ispra, Italy
| | - Jason M. O’Brien
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON, Canada
| | - Nathan L. Pollesch
- United States Environmental Protection Agency, Mid-Continent Ecology Division, Duluth, MN, USA
| | - L. Cody Smith
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, People’s Republic of China
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium
| |
Collapse
|
216
|
Robinson S, Nevalainen J, Pinna G, Campalans A, Radicella JP, Guyon L. Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields. Bioinformatics 2018; 33:i170-i179. [PMID: 28881978 PMCID: PMC5870666 DOI: 10.1093/bioinformatics/btx244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Motivation Incorporating gene interaction data into the identification of ‘hit’ genes in genomic experiments is a well-established approach leveraging the ‘guilt by association’ assumption to obtain a network based hit list of functionally related genes. We aim to develop a method to allow for multivariate gene scores and multiple hit labels in order to extend the analysis of genomic screening data within such an approach. Results We propose a Markov random field-based method to achieve our aim and show that the particular advantages of our method compared with those currently used lead to new insights in previously analysed data as well as for our own motivating data. Our method additionally achieves the best performance in an independent simulation experiment. The real data applications we consider comprise of a survival analysis and differential expression experiment and a cell-based RNA interference functional screen. Availability and implementation We provide all of the data and code related to the results in the paper. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Sean Robinson
- CEA, BIG, Biologie à Grande Echelle, F-38054 Grenoble, France.,Université Grenoble-Alpes, F-38000 Grenoble, France.,INSERM, U1038, F-38054 Grenoble, France.,Department of Mathematics and Statistics, University of Turku, Turku, Finland.,Industrial Biotechnology, VTT Technical Research Centre of Finland, Turku, Finland
| | - Jaakko Nevalainen
- Department of Mathematics and Statistics, University of Turku, Turku, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Guillaume Pinna
- Plateforme ARN Interférence (PArI), DSV/ISVFJ/SBIGEM/UMR 9198 I2BC, CEA Saclay, Gif-sur-Yvette, France
| | - Anna Campalans
- Institute of Molecular and Cellular Radiobiology, CEA, Fontenay-aux-Roses, France.,INSERM, U967, Fontenay-aux-Roses, France.,Université Paris Diderot, U967, Fontenay-aux-Roses, France.,Université Paris Sud, U967, Fontenay-aux-Roses, France
| | - J Pablo Radicella
- Institute of Molecular and Cellular Radiobiology, CEA, Fontenay-aux-Roses, France.,INSERM, U967, Fontenay-aux-Roses, France.,Université Paris Diderot, U967, Fontenay-aux-Roses, France.,Université Paris Sud, U967, Fontenay-aux-Roses, France
| | - Laurent Guyon
- CEA, BIG, Biologie à Grande Echelle, F-38054 Grenoble, France.,Université Grenoble-Alpes, F-38000 Grenoble, France.,INSERM, U1038, F-38054 Grenoble, France
| |
Collapse
|
217
|
Couto CMV, Comin CH, Costa LDF. Effects of threshold on the topology of gene co-expression networks. MOLECULAR BIOSYSTEMS 2018; 13:2024-2035. [PMID: 28770908 DOI: 10.1039/c7mb00101k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Several developments regarding the analysis of gene co-expression profiles using complex network theory have been reported recently. Such approaches usually start with the construction of an unweighted gene co-expression network, therefore requiring the selection of a suitable threshold defining which pairs of vertices will be connected. We aimed at addressing such an important problem by suggesting and comparing five different approaches for threshold selection. Each of the methods considers a respective biologically-motivated criterion for electing a potentially suitable threshold. A set of 21 microarray experiments from different biological groups was used to investigate the effect of applying the five proposed criteria to several biological situations. For each experiment, we used the Pearson correlation coefficient to measure the relationship between each gene pair, and the resulting weight matrices were thresholded considering several values, generating respective adjacency matrices (co-expression networks). Each of the five proposed criteria was then applied in order to select the respective threshold value. The effects of these thresholding approaches on the topology of the resulting networks were compared by using several measurements, and we verified that, depending on the database, the impact on the topological properties can be large. However, a group of databases was verified to be similarly affected by most of the considered criteria. Based on such results, it can be suggested that when the generated networks present similar measurements, the thresholding method can be chosen with greater freedom. If the generated networks are markedly different, the thresholding method that better suits the interests of each specific research study represents a reasonable choice.
Collapse
|
218
|
Motieghader H, Kouhsar M, Najafi A, Sadeghi B, Masoudi-Nejad A. mRNA-miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation. MOLECULAR BIOSYSTEMS 2018; 13:2168-2180. [PMID: 28861579 DOI: 10.1039/c7mb00400a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biomarker detection is one of the most important and challenging problems in cancer studies. Recently, non-coding RNA based biomarkers such as miRNA expression levels have been used for early diagnosis of many cancer types. In this study, a systems biology approach was used to detect novel miRNA based biomarkers for CRC diagnosis in early stages. The mRNA expression data from three CRC stages (Low-grade Intraepithelial Neoplasia (LIN), High-grade Intraepithelial Neoplasia (HIN) and Adenocarcinoma) were used to reconstruct co-expression networks. The networks were clustered to extract co-expression modules and detected low preserved modules among CRC stages. Then, the experimentally validated mRNA-miRNA interaction data were applied to reconstruct three mRNA-miRNA bipartite networks. Twenty miRNAs with the highest degree (hub miRNAs) were selected in each bipartite network to reconstruct three bipartite subnetworks for further analysis. The analysis of these hub miRNAs in the bipartite subnetworks revealed 30 distinct important miRNAs as prognostic markers in CRC stages. There are two novel CRC related miRNAs (hsa-miR-190a-3p and hsa-miR-1277-5p) in these 30 hub miRNAs that have not been previously reported in CRC. Furthermore, a drug-gene interaction network was reconstructed to detect potential candidate drugs for CRC treatment. Our analysis shows that the hub miRNAs in the mRNA-miRNA bipartite network are very essential in CRC progression and should be investigated precisely in future studies. In addition, there are many important target genes in the results that may be critical in CRC progression and can be analyzed as therapeutic targets in future research.
Collapse
Affiliation(s)
- Habib Motieghader
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | | | | | | | | |
Collapse
|
219
|
Woidy M, Muntau AC, Gersting SW. Inborn errors of metabolism and the human interactome: a systems medicine approach. J Inherit Metab Dis 2018; 41:285-296. [PMID: 29404805 PMCID: PMC5959957 DOI: 10.1007/s10545-018-0140-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 01/01/2018] [Accepted: 01/10/2018] [Indexed: 12/14/2022]
Abstract
The group of inborn errors of metabolism (IEM) displays a marked heterogeneity and IEM can affect virtually all functions and organs of the human organism; however, IEM share that their associated proteins function in metabolism. Most proteins carry out cellular functions by interacting with other proteins, and thus are organized in biological networks. Therefore, diseases are rarely the consequence of single gene mutations but of the perturbations caused in the related cellular network. Systematic approaches that integrate multi-omics and database information into biological networks have successfully expanded our knowledge of complex disorders but network-based strategies have been rarely applied to study IEM. We analyzed IEM on a proteome scale and found that IEM-associated proteins are organized as a network of linked modules within the human interactome of protein interactions, the IEM interactome. Certain IEM disease groups formed self-contained disease modules, which were highly interlinked. On the other hand, we observed disease modules consisting of proteins from many different disease groups in the IEM interactome. Moreover, we explored the overlap between IEM and non-IEM disease genes and applied network medicine approaches to investigate shared biological pathways, clinical signs and symptoms, and links to drug targets. The provided resources may help to elucidate the molecular mechanisms underlying new IEM, to uncover the significance of disease-associated mutations, to identify new biomarkers, and to develop novel therapeutic strategies.
Collapse
Affiliation(s)
- Mathias Woidy
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Ania C Muntau
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Søren W Gersting
- Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Lindwurmstrasse 4, 80336, Munich, Germany.
| |
Collapse
|
220
|
Ramakrishnan V, Mager DE. Network-Based Analysis of Bortezomib Pharmacodynamic Heterogeneity in Multiple Myeloma Cells. J Pharmacol Exp Ther 2018; 365:734-751. [PMID: 29632237 DOI: 10.1124/jpet.118.247924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022] Open
Abstract
The objective of this study is to evaluate the heterogeneity in pharmacodynamic response in four in vitro multiple myeloma cell lines to treatment with bortezomib, and to assess whether such differences are associated with drug-induced intracellular signaling protein dynamics identified via a logic-based network modeling approach. The in vitro pharmacodynamic-efficacy of bortezomib was evaluated through concentration-effect and cell proliferation dynamical studies in U266, RPMI8226, MM.1S, and NCI-H929 myeloma cell lines. A Boolean logic-based network model incorporating intracellular protein signaling pathways relevant to myeloma cell growth, proliferation, and apoptosis was developed based on information available in the literature and used to identify key proteins regulating bortezomib pharmacodynamics. The time-course of network-identified proteins was measured using the MAGPIX protein assay system. Traditional pharmacodynamic modeling endpoints revealed variable responses of the cell lines to bortezomib treatment, classifying cell lines as more sensitive (MM.1S and NCI-H929) and less sensitive (U266 and RPMI8226). Network centrality and model reduction identified key proteins (e.g., phosphorylated nuclear factor-κB, phosphorylated protein kinase B, phosphorylated mechanistic target of rapamycin, Bcl-2, phosphorylated c-Jun N-terminal kinase, phosphorylated p53, p21, phosphorylated Bcl-2-associated death promoter, caspase 8, and caspase 9) that govern bortezomib pharmacodynamics. The corresponding relative expression (normalized to 0-hour untreated-control cells) of proteins demonstrated a greater magnitude and earlier onset of stimulation/inhibition in cells more sensitive (MM.1S and NCI-H929) to bortezomib-induced cell death at 20 nM, relative to the less sensitive cells (U266 and RPMI8226). Overall, differences in intracellular signaling appear to be associated with bortezomib pharmacodynamic heterogeneity, and key proteins may be potential biomarkers to evaluate bortezomib responses.
Collapse
Affiliation(s)
- Vidya Ramakrishnan
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, New York
| | - Donald E Mager
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, New York
| |
Collapse
|
221
|
Nuncia-Cantarero M, Martinez-Canales S, Andrés-Pretel F, Santpere G, Ocaña A, Galan-Moya EM. Functional transcriptomic annotation and protein-protein interaction network analysis identify NEK2, BIRC5, and TOP2A as potential targets in obese patients with luminal A breast cancer. Breast Cancer Res Treat 2018; 168:613-623. [PMID: 29330624 PMCID: PMC5842257 DOI: 10.1007/s10549-017-4652-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/29/2017] [Indexed: 12/22/2022]
Abstract
PURPOSE Although obesity is a risk factor for breast cancer, little effort has been made in the identification of druggable molecular alterations in obese-breast cancer patients. Tumors are controlled by their surrounding microenvironment, in which the adipose tissue is a main component. In this work, we intended to describe molecular alterations at a transcriptomic and protein-protein interaction (PPI) level between obese and non-obese patients. METHODS AND RESULTS Gene expression data of 269 primary breast tumors were compared between normal-weight (BMI < 25, n = 130) and obese (IMC > 30, n = 139) patients. No significant differences were found for the global breast cancer population. However, within the luminal A subtype, upregulation of 81 genes was observed in the obese group (FC ≥ 1.4). Next, we explored the association of these genes with patient outcome, observing that 39 were linked with detrimental outcome. Their PPI map formed highly compact cluster and functional annotation analyses showed that cell cycle, cell proliferation, cell differentiation, and cellular response to extracellular stimuli were the more altered functions. Combined analyses of genes within the described functions are correlated with poor outcome. PPI network analyses for each function were to search for druggable opportunities. We identified 16 potentially druggable candidates. Among them, NEK2, BIRC5, and TOP2A were also found to be amplified in breast cancer, suggesting that they could act as strategic players in the obese-deregulated transcriptome. CONCLUSION In summary, our in silico analysis describes molecular alterations of luminal A tumors and proposes a druggable PPI network in obese patients with potential for translation to the clinical practice.
Collapse
Affiliation(s)
- Miriam Nuncia-Cantarero
- Translational Oncology Laboratory, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha (UCLM), C/Almansa 14, 02008, Albacete, Spain
| | | | | | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Alberto Ocaña
- Translational Research Unit, University Hospital, Albacete, Spain
| | - Eva Maria Galan-Moya
- Translational Oncology Laboratory, Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla La Mancha (UCLM), C/Almansa 14, 02008, Albacete, Spain.
| |
Collapse
|
222
|
Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG. Bipartite graphs in systems biology and medicine: a survey of methods and applications. Gigascience 2018; 7:1-31. [PMID: 29648623 PMCID: PMC6333914 DOI: 10.1093/gigascience/giy014] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 01/15/2018] [Accepted: 02/13/2018] [Indexed: 11/14/2022] Open
Abstract
The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.
Collapse
Affiliation(s)
- Georgios A Pavlopoulos
- Lawrence Berkeley Labs, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Panagiota I Kontou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylül University, 35340, Turkey
| | - Costas Bouyioukos
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, France
| | - Evripides Markou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
| | - Pantelis G Bagos
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
| |
Collapse
|
223
|
Dos Santos Vasconcelos CR, de Lima Campos T, Rezende AM. Building protein-protein interaction networks for Leishmania species through protein structural information. BMC Bioinformatics 2018; 19:85. [PMID: 29510668 PMCID: PMC5840830 DOI: 10.1186/s12859-018-2105-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/01/2018] [Indexed: 12/21/2022] Open
Abstract
Background Systematic analysis of a parasite interactome is a key approach to understand different biological processes. It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum. These parasites cause Leishmaniasis, a worldwide distributed and neglected disease, with limited treatment options using currently available drugs. Results The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. In addition, we trained a machine-learning algorithm (Gradient Boosting) using docking information performed on a curated set of positive and negative protein interaction data. Our final model obtained an AUC = 0.88, with recall = 0.69, specificity = 0.88 and precision = 0.83. Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis, and 708 protein structures and 7391 protein interactions for L. infantum. The predicted networks were integrated to protein interaction data already available, analyzed using several topological features and used to classify proteins as essential for network stability. Conclusions The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported. Electronic supplementary material The online version of this article (10.1186/s12859-018-2105-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Crhisllane Rafaele Dos Santos Vasconcelos
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Genetics Department of Universidade Federal de Pernambuco, Recife, PE, Brazil.
| | - Túlio de Lima Campos
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil.,Bioinformatics Plataform of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil
| | - Antonio Mauro Rezende
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Bioinformatics Plataform of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Genetics Department of Universidade Federal de Pernambuco, Recife, PE, Brazil.
| |
Collapse
|
224
|
Sato JR, Biazoli CE, Salum GA, Gadelha A, Crossley N, Vieira G, Zugman A, Picon FA, Pan PM, Hoexter MQ, Amaro E, Anés M, Moura LM, Del'Aquilla MAG, Mcguire P, Rohde LA, Miguel EC, Jackowski AP, Bressan RA. Association between abnormal brain functional connectivity in children and psychopathology: A study based on graph theory and machine learning. World J Biol Psychiatry 2018. [PMID: 28635541 DOI: 10.1080/15622975.2016.1274050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES One of the major challenges facing psychiatry is how to incorporate biological measures in the classification of mental health disorders. Many of these disorders affect brain development and its connectivity. In this study, we propose a novel method for assessing brain networks based on the combination of a graph theory measure (eigenvector centrality) and a one-class support vector machine (OC-SVM). METHODS We applied this approach to resting-state fMRI data from 622 children and adolescents. Eigenvector centrality (EVC) of nodes from positive- and negative-task networks were extracted from each subject and used as input to an OC-SVM to label individual brain networks as typical or atypical. We hypothesised that classification of these subjects regarding the pattern of brain connectivity would predict the level of psychopathology. RESULTS Subjects with atypical brain network organisation had higher levels of psychopathology (p < 0.001). There was a greater EVC in the typical group at the bilateral posterior cingulate and bilateral posterior temporal cortices; and significant decreases in EVC at left temporal pole. CONCLUSIONS The combination of graph theory methods and an OC-SVM is a promising method to characterise neurodevelopment, and may be useful to understand the deviations leading to mental disorders.
Collapse
Affiliation(s)
- João Ricardo Sato
- a Center of Mathematics, Computation and Cognition, Universidade Federal do ABC , Santo André , Brazil.,b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,c Department of Radiology , School of Medicine, University of Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| | - Claudinei Eduardo Biazoli
- a Center of Mathematics, Computation and Cognition, Universidade Federal do ABC , Santo André , Brazil.,c Department of Radiology , School of Medicine, University of Sao Paulo , Brazil
| | - Giovanni Abrahão Salum
- d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil.,e Hospital de Clinicas de Porto Alegre and Department of Psychiatry , Federal University of Rio Grande do Sul , Porto Alegre , Brazil
| | - Ary Gadelha
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| | - Nicolas Crossley
- f Department of Psychosis Studies, Institute of Psychiatry, King's College London , United Kingdom
| | - Gilson Vieira
- c Department of Radiology , School of Medicine, University of Sao Paulo , Brazil.,g Bioinformatics Program , Institute of Mathematics and Statistics, University of Sao Paulo , Brazil
| | - André Zugman
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| | - Felipe Almeida Picon
- d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil.,e Hospital de Clinicas de Porto Alegre and Department of Psychiatry , Federal University of Rio Grande do Sul , Porto Alegre , Brazil
| | - Pedro Mario Pan
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| | - Marcelo Queiroz Hoexter
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil.,h Department of Psychiatry , School of Medicine, University of Sao Paulo , Brazil
| | - Edson Amaro
- i Institute of Radiology (InRad), Faculdade de Medicina , Universidade de Sao Paulo , Brazil
| | - Mauricio Anés
- d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil.,e Hospital de Clinicas de Porto Alegre and Department of Psychiatry , Federal University of Rio Grande do Sul , Porto Alegre , Brazil
| | - Luciana Monteiro Moura
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| | - Marco Antonio Gomes Del'Aquilla
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| | - Philip Mcguire
- f Department of Psychosis Studies, Institute of Psychiatry, King's College London , United Kingdom
| | - Luis Augusto Rohde
- d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil.,e Hospital de Clinicas de Porto Alegre and Department of Psychiatry , Federal University of Rio Grande do Sul , Porto Alegre , Brazil
| | - Euripedes Constantino Miguel
- d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil.,h Department of Psychiatry , School of Medicine, University of Sao Paulo , Brazil
| | - Andrea Parolin Jackowski
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| | - Rodrigo Affonseca Bressan
- b Department of Psychiatry, Interdisciplinary Lab for Clinical Neurosciences (LiNC) , Universidade Federal de Sao Paulo (UNIFESP) , Sao Paulo , Brazil.,d National Institute of Developmental Psychiatry for Children and Adolescents , CNPq , Brazil
| |
Collapse
|
225
|
Rudd TR, Preston MD, Yates EA. The nature of the conserved basic amino acid sequences found among 437 heparin binding proteins determined by network analysis. MOLECULAR BIOSYSTEMS 2018; 13:852-865. [PMID: 28317949 DOI: 10.1039/c6mb00857g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In multicellular organisms, a large number of proteins interact with the polyanionic polysaccharides heparan sulphate (HS) and heparin. These interactions are usually assumed to be dominated by charge-charge interactions between the anionic carboxylate and/or sulfate groups of the polysaccharide and cationic amino acids of the protein. A major question is whether there exist conserved amino acid sequences for HS/heparin binding among these diverse proteins. Potentially conserved HS/heparin binding sequences were sought amongst 437 HS/heparin binding proteins. Amino acid sequences were extracted and compared using a Levenshtein distance metric. The resultant similarity matrices were visualised as graphs, enabling extraction of strongly conserved sequences from highly variable primary sequences while excluding short, core regions. This approach did not reveal extensive, conserved HS/heparin binding sequences, rather a number of shorter, more widely spaced sequences that may work in unison to form heparin-binding sites on protein surfaces, arguing for convergent evolution. Thus, it is the three-dimensional arrangement of these conserved motifs on the protein surface, rather than the primary sequence per se, which are the evolutionary elements.
Collapse
Affiliation(s)
- Timothy R Rudd
- The National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| | | | | |
Collapse
|
226
|
Integrated Systems and Chemical Biology Approach for Targeted Therapies. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|
227
|
Fiandaca MS, Mapstone M, Connors E, Jacobson M, Monuki ES, Malik S, Macciardi F, Federoff HJ. Systems healthcare: a holistic paradigm for tomorrow. BMC SYSTEMS BIOLOGY 2017; 11:142. [PMID: 29258513 PMCID: PMC5738174 DOI: 10.1186/s12918-017-0521-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 12/01/2017] [Indexed: 12/13/2022]
Abstract
Systems healthcare is a holistic approach to health premised on systems biology and medicine. The approach integrates data from molecules, cells, organs, the individual, families, communities, and the natural and man-made environment. Both extrinsic and intrinsic influences constantly challenge the biological networks associated with wellness. Such influences may dysregulate networks and allow pathobiology to evolve, resulting in early clinical presentation that requires astute assessment and timely intervention for successful mitigation. Herein, we describe the components of relevant biological systems and the nature of progression from at-risk to manifest disease. We illustrate the systems approach by examining two relevant clinical examples: Alzheimer's and cardiovascular diseases. The implications of systems healthcare management are examined through the lens of economics, ethics, policy and the law. Finally, we propose the need to develop new educational paradigms to enhance the training of the health professional in an era of systems medicine.
Collapse
Affiliation(s)
- Massimo S Fiandaca
- Department of Neurology, School of Medicine, Irvine, USA
- Department of Neurological Surgery, School of Medicine, Irvine, USA
- Department of Anatomy & Neurobiology, School of Medicine, Irvine, USA
| | - Mark Mapstone
- Department of Neurology, School of Medicine, Irvine, USA
| | | | - Mireille Jacobson
- Department of Economics, Paul Merage School of Business, Irvine, USA
| | - Edwin S Monuki
- Department of Pathology & Laboratory Medicine, School of Medicine, Irvine, USA
| | - Shaista Malik
- Department of Medicine, School of Medicine, Irvine, USA
| | - Fabio Macciardi
- Department of Psychiatry & Human Behavior, School of Medicine, Irvine, USA
| | - Howard J Federoff
- Department of Neurology, School of Medicine, Irvine, USA.
- University of California Irvine (UCI), Irvine, CA, USA.
| |
Collapse
|
228
|
Schrom EC, Prada JM, Graham AL. Immune Signaling Networks: Sources of Robustness and Constrained Evolvability during Coevolution. Mol Biol Evol 2017; 35:676-687. [PMID: 29294066 DOI: 10.1093/molbev/msx321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Defense against infection incurs costs as well as benefits that are expected to shape the evolution of optimal defense strategies. In particular, many theoretical studies have investigated contexts favoring constitutive versus inducible defenses. However, even when one immune strategy is theoretically optimal, it may be evolutionarily unachievable. This is because evolution proceeds via mutational changes to the protein interaction networks underlying immune responses, not by changes to an immune strategy directly. Here, we use a theoretical simulation model to examine how underlying network architectures constrain the evolution of immune strategies, and how these network architectures account for desirable immune properties such as inducibility and robustness. We focus on immune signaling because signaling molecules are common targets of parasitic interference but are rarely studied in this context. We find that in the presence of a coevolving parasite that disrupts immune signaling, hosts evolve constitutive defenses even when inducible defenses are theoretically optimal. This occurs for two reasons. First, there are relatively few network architectures that produce immunity that is both inducible and also robust against targeted disruption. Second, evolution toward these few robust inducible network architectures often requires intermediate steps that are vulnerable to targeted disruption. The few networks that are both robust and inducible consist of many parallel pathways of immune signaling with few connections among them. In the context of relevant empirical literature, we discuss whether this is indeed the most evolutionarily accessible robust inducible network architecture in nature, and when it can evolve.
Collapse
Affiliation(s)
- Edward C Schrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Joaquín M Prada
- Mathematics Institute, University of Warwick, Coventry, United Kingdom.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| |
Collapse
|
229
|
Shen PC, Hour AL, Liu LYD. Microarray meta-analysis to explore abiotic stress-specific gene expression patterns in Arabidopsis. BOTANICAL STUDIES 2017; 58:22. [PMID: 28510204 PMCID: PMC5432924 DOI: 10.1186/s40529-017-0176-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/05/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants' adaptations to stresses using few datasets might overlook the different aspects of stress tolerance in plants, which might be simultaneously and consequently operated in the system. Fortunately, the accumulated microarray expression data offer an opportunity to infer abiotic stress-specific gene expression patterns through meta-analysis. In this study, we propose to combine microarray gene expression data under control, cold, drought, heat, and salt conditions and determined modules (gene sets) of genes highly associated with each other according to the observed expression data. RESULTS By analyzing the expression variations of the Eigen genes from different conditions, we had identified two, three, and five gene modules as cold-, heat-, and salt-specific modules, respectively. Most of the cold- or heat-specific modules were differentially expressed to a particular degree in shoot samples, while most of the salt-specific modules were differentially expressed to a particular degree in root samples. A gene ontology (GO) analysis on the stress-specific modules suggested that the gene modules exclusively enriched stress-related GO terms and that different genes under the same GO terms may be alternatively disturbed in different conditions. The gene regulatory events for two genes, DREB1A and DEAR1, in the cold-specific gene module had also been validated, as evidenced through the literature search. CONCLUSIONS Our protocols study the specificity of the gene modules that were specifically activated under a particular type of abiotic stress. The biplot can also assist to visualize the stress-specific gene modules. In conclusion, our approach has the potential to further elucidate mechanisms in plants and beneficial for future experiments design under different abiotic stresses.
Collapse
Affiliation(s)
- Po-chih Shen
- Biometrics Division, Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ai-ling Hour
- Department of Life Science, Fu-Jen Catholic University, Xinbei, Taiwan
| | - Li-yu Daisy Liu
- Biometrics Division, Department of Agronomy, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
230
|
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.
Collapse
|
231
|
Palmieri O, Mazza T, Castellana S, Panza A, Latiano T, Corritore G, Andriulli A, Latiano A. Inflammatory Bowel Disease Meets Systems Biology: A Multi-Omics Challenge and Frontier. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:692-698. [PMID: 27930092 DOI: 10.1089/omi.2016.0147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inflammatory bowel disease (IBD) is a systemic disease that is characterized by the inflammation of the gastrointestinal tract. It includes ulcerative colitis and the Crohn's disease. Presently, IBD is one of the most investigated common complex human disorders, although its causes remain unclear. Multi-omics mechanisms involving genomic, transcriptomic, proteomic, and epigenomic variations, not to forget the miRNome, together with environmental contributions, result in an impairment of the immune system in persons with IBD. Such interactions at multiple levels of biology and in concert with the environment constitute the actual engine of this complex disease, demanding a multifactorial and multi-omics perspective to better understand the root causes of IBD. This expert analysis reviews and examines the latest literature and underscores, from the perspective of systems biology, the value of multi-omics technologies as opportunities to unravel the "IBD integrome." We anticipate that multi-omics research will accelerate the new discoveries and insights on IBD in the near future. It shall also pave the way for early diagnosis and help clinicians and families with IBD to forecast and make informed decisions about the prognosis and, possibly, personalized therapeutics in the future.
Collapse
Affiliation(s)
- Orazio Palmieri
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Stefano Castellana
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Panza
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tiziana Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Giuseppe Corritore
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Angelo Andriulli
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| |
Collapse
|
232
|
Koirala N, Fleischer V, Glaser M, Zeuner KE, Deuschl G, Volkmann J, Muthuraman M, Groppa S. Frontal Lobe Connectivity and Network Community Characteristics are Associated with the Outcome of Subthalamic Nucleus Deep Brain Stimulation in Patients with Parkinson's Disease. Brain Topogr 2017; 31:311-321. [PMID: 28986718 DOI: 10.1007/s10548-017-0597-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/26/2017] [Indexed: 12/23/2022]
Abstract
Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is nowadays an evidence-based state of the art therapy option for motor and non-motor symptoms in patients with Parkinson's disease (PD). However, the exact anatomical regions of the cerebral network that are targeted by STN-DBS have not been precisely described and no definitive pre-intervention predictors of the clinical response exist. In this study, we test the hypothesis that the clinical effectiveness of STN-DBS depends on the connectivity profile of the targeted brain networks. Therefore, we used diffusion-weighted imaging (DWI) and probabilistic tractography to reconstruct the anatomical networks and the graph theoretical framework to quantify the connectivity profile. DWI was obtained pre-operatively from 15 PD patients who underwent DBS (mean age = 67.87 ± 7.88, 11 males, H&Y score = 3.5 ± 0.8) using a 3T MRI scanner (Philips Achieva). The pre-operative connectivity properties of a network encompassing frontal, prefrontal cortex and cingulate gyrus were directly linked to the postoperative clinical outcome. Eccentricity as a topological-characteristic of the network defining how cerebral regions are embedded in relation to distant sites correlated inversely with the applied voltage at the active electrode for optimal clinical response. We found that network topology and pre-operative connectivity patterns have direct influence on the clinical response to DBS and may serve as important and independent predictors of the postoperative clinical outcome.
Collapse
Affiliation(s)
- Nabin Koirala
- Department of Neurology, Johannes Gutenberg University, 55131, Mainz, Germany
| | - Vinzenz Fleischer
- Department of Neurology, Johannes Gutenberg University, 55131, Mainz, Germany
| | - Martin Glaser
- Department of Neurosurgery, Johannes Gutenberg University, 55131, Mainz, Germany
| | - Kirsten E Zeuner
- Department of Neurology, University of Kiel, 24105, Kiel, Germany
| | - Günther Deuschl
- Department of Neurology, University of Kiel, 24105, Kiel, Germany
| | - Jens Volkmann
- Department of Neurology, University of Würzburg, 97080, Würzburg, Germany
| | | | - Sergiu Groppa
- Department of Neurology, Johannes Gutenberg University, 55131, Mainz, Germany.
| |
Collapse
|
233
|
Jiao X, Ranganathan S. Prediction of interface residue based on the features of residue interaction network. J Theor Biol 2017; 432:49-54. [PMID: 28818468 DOI: 10.1016/j.jtbi.2017.08.014] [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] [Received: 04/18/2017] [Revised: 07/31/2017] [Accepted: 08/13/2017] [Indexed: 10/19/2022]
Abstract
Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model.
Collapse
Affiliation(s)
- Xiong Jiao
- Institute of Applied Mechanics and Biomedical Engineering, College of Mechanics, Taiyuan University of Technology, Taiyuan 030024, China; Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| |
Collapse
|
234
|
Kuang J, Cadotte MW, Chen Y, Shu H, Liu J, Chen L, Hua Z, Shu W, Zhou J, Huang L. Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly. Front Microbiol 2017; 8:1486. [PMID: 28848508 PMCID: PMC5554326 DOI: 10.3389/fmicb.2017.01486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/24/2017] [Indexed: 11/29/2022] Open
Abstract
Understanding microbial interactions is essential to decipher the mechanisms of community assembly and their effects on ecosystem functioning, however, the conservation of species- and trait-based network interactions along environmental gradient remains largely unknown. Here, by using the network-based analyses with three paralleled data sets derived from 16S rRNA gene pyrosequencing, functional microarray, and predicted metagenome, we test our hypothesis that the network interactions of traits are more conserved than those of taxonomic measures, with significantly lower variation of network characteristics along the environmental gradient in acid mine drainage. The results showed that although the overall network characteristics remained similar, the structural variation was significantly lower at trait levels. The higher conserved individual node topological properties at trait level rather than at species level indicated that the responses of diverse traits remained relatively consistent even though different species played key roles under different environmental conditions. Additionally, the randomization tests revealed that it could not reject the null hypothesis that species-based correlations were random, while the tests suggested that correlation patterns of traits were non-random. Furthermore, relationships between trait-based network characteristics and environmental properties implied that trait-based networks might be more useful in reflecting the variation of ecosystem function. Taken together, our results suggest that deterministic trait-based community assembly results in greater conservation of network interaction, which may ensure ecosystem function across environmental regimes, emphasizing the potential importance of measuring the complexity and conservation of network interaction in evaluating the ecosystem stability and functioning.
Collapse
Affiliation(s)
- Jialiang Kuang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States
| | - Marc W Cadotte
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China.,Department of Biological Sciences, University of Toronto-ScarboroughToronto, ON, Canada.,Ecology and Evolutionary Biology, University of TorontoToronto, ON, Canada
| | - Yongjian Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Haoyue Shu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Linxing Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Zhengshuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Wensheng Shu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States.,Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, United States.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Linan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| |
Collapse
|
235
|
Alvarez-Silva MC, Álvarez-Yela AC, Gómez-Cano F, Zambrano MM, Husserl J, Danies G, Restrepo S, González-Barrios AF. Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils. PLoS One 2017; 12:e0181826. [PMID: 28767679 PMCID: PMC5540551 DOI: 10.1371/journal.pone.0181826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/09/2017] [Indexed: 01/02/2023] Open
Abstract
Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.
Collapse
Affiliation(s)
- María Camila Alvarez-Silva
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Astrid Catalina Álvarez-Yela
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Fabio Gómez-Cano
- Laboratorio de Micología y Fitopatología (LAMFU), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - María Mercedes Zambrano
- Center for Genomics and Bioinformatics of Extreme Environments (Gebix), Bogotá, Colombia
- Corporación Corpogen Research Center, Bogotá, Colombia
| | - Johana Husserl
- Centro de Investigaciones en Ingeniería Ambiental, Department of Environmental Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Giovanna Danies
- Laboratorio de Micología y Fitopatología (LAMFU), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología (LAMFU), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | |
Collapse
|
236
|
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. Adv Bioinformatics 2017; 2017:1278932. [PMID: 28804499 PMCID: PMC5540468 DOI: 10.1155/2017/1278932] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/14/2017] [Accepted: 06/04/2017] [Indexed: 12/19/2022] Open
Abstract
Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today's indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. We comment on their strengths and their weaknesses and empirically discuss their scalability, user friendliness, and postvisualization capabilities.
Collapse
|
237
|
Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos GA. NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks. BMC Res Notes 2017; 10:278. [PMID: 28705239 PMCID: PMC5513407 DOI: 10.1186/s13104-017-2607-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/07/2017] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. RESULTS Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .
Collapse
Affiliation(s)
- Theodosios Theodosiou
- Bioinformatics & Computational Biology Laboratory, Division of Basic Sciences, University of Crete Medical School, 70013 Heraklion, Crete, Greece
| | - Georgios Efstathiou
- Bioinformatics & Computational Biology Laboratory, Division of Basic Sciences, University of Crete Medical School, 70013 Heraklion, Crete, Greece
| | - Nikolas Papanikolaou
- Bioinformatics & Computational Biology Laboratory, Division of Basic Sciences, University of Crete Medical School, 70013 Heraklion, Crete, Greece
| | - Nikos C Kyrpides
- Joint Genome Institute, Lawrence Berkeley Lab, United States Department of Energy, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, Galaneika, 35100, Lamia, Greece
| | - Ioannis Iliopoulos
- Bioinformatics & Computational Biology Laboratory, Division of Basic Sciences, University of Crete Medical School, 70013 Heraklion, Crete, Greece.
| | - Georgios A Pavlopoulos
- Bioinformatics & Computational Biology Laboratory, Division of Basic Sciences, University of Crete Medical School, 70013 Heraklion, Crete, Greece. .,Joint Genome Institute, Lawrence Berkeley Lab, United States Department of Energy, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| |
Collapse
|
238
|
Niedzwiecki MM, Miller GW. The Exposome Paradigm in Human Health: Lessons from the Emory Exposome Summer Course. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:064502. [PMID: 28669935 PMCID: PMC5743443 DOI: 10.1289/ehp1712] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/02/2017] [Accepted: 02/12/2017] [Indexed: 05/18/2023]
Abstract
The environment plays a major role in human health, yet tools to study the health impacts of complex environmental exposures are lacking. In 2005, Christopher Wild introduced the concept of the exposome, which encompasses environmental exposures and concomitant biological responses throughout the life course. Exposome-based approaches have the potential to enable novel insights into numerous research questions in environmental health sciences. To promote and develop the concept of the exposome, the Health and Exposome Research Center: Understanding Lifetime Exposures (HERCULES) Exposome Research Center at Emory University held the first Emory Exposome Summer Course from 13-17 June 2016. https://doi.org/10.1289/EHP1712.
Collapse
Affiliation(s)
- Megan M Niedzwiecki
- Department of Environmental Health, Rollins School of Public Health, Emory University , Atlanta, Georgia, USA
| | - Gary W Miller
- Department of Environmental Health, Rollins School of Public Health, Emory University , Atlanta, Georgia, USA
| |
Collapse
|
239
|
Singh P, Golla N, Singh P, Baddela VS, Chand S, Baithalu RK, Singh D, Onteru SK. Salivary miR-16, miR-191 and miR-223: intuitive indicators of dominant ovarian follicles in buffaloes. Mol Genet Genomics 2017; 292:935-953. [PMID: 28447195 DOI: 10.1007/s00438-017-1323-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 04/18/2017] [Indexed: 11/30/2022]
Abstract
Estrus or sexual receptivity determination is utmost important for efficient breeding programs for female buffaloes. Prominent estrus behavioral symptoms are the result of several molecular and neuroendocrine events involving the ovary and the brain. Expression of estrus behavior is poor in buffaloes during the summer season. Hence, the discovery of biomarkers specific to the estrus stage or its related ovarian events, like the presence of dominant ovarian follicle, is helpful for developing an easy estrus determination method. MicroRNA are small non-coding RNA with a potential to be biomarkers. Therefore, the present study targeted to investigate the potential of estrogen responsive miRNAs (miR-24, miR-200c, miR-16, miR-191, miR-223 and miR-203) as estrus biomarkers in buffalo saliva, a non-invasive fluid representing animals' pathophysiology. There was a significant (P < 0.05) increase in the salivary presence of the miR-16, miR-191 and miR-223 at 6th and 18th-19th days than the 0 day (estrus), 10th day and the following consecutive estrus day. These observations may indicate an association between the representative lower presence of these miRNA in saliva and the presence of dominant ovarian follicles. To test this association, pathway analysis, target gene identification, functional annotation and protein-protein interaction networks (PPI) were performed for miR-16, miR-191 and miR-223 by different bioinformatics tools. Interestingly, the top pathways (fatty acid biosynthesis and oocyte meiosis), target genes (FGF, BDNF and IGF1) and PPI hub genes (KRAS, BCL2 and IGF1) of these miRNAs were found essential for ovarian follicular dominance. In conclusion, the miR-16, miR-191 and miR-223 may not be the perfect estrus stage-specific biomarkers. However, their lower presence in saliva at estrus and 9th-10th day of estrous cycles, when the ovary usually has a dominant follicle in buffaloes, may intuitively indicate the follicular dominance. Further studies are needed to prove this association in a large population.
Collapse
Affiliation(s)
- Prashant Singh
- Molecular Endocrinology, Functional Genomics and Systems Biology Lab, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Naresh Golla
- Molecular Endocrinology, Functional Genomics and Systems Biology Lab, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Pankaj Singh
- Molecular Endocrinology, Functional Genomics and Systems Biology Lab, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Vijay Simha Baddela
- Molecular Endocrinology, Functional Genomics and Systems Biology Lab, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Subhash Chand
- AI Lab, Artificial Breeding Research Center, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Rubina Kumari Baithalu
- Livestock Production and Management, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Dheer Singh
- Molecular Endocrinology, Functional Genomics and Systems Biology Lab, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Suneel Kumar Onteru
- Molecular Endocrinology, Functional Genomics and Systems Biology Lab, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, 132001, India.
| |
Collapse
|
240
|
Yoon BH, Kim SK, Kim SY. Use of Graph Database for the Integration of Heterogeneous Biological Data. Genomics Inform 2017; 15:19-27. [PMID: 28416946 PMCID: PMC5389944 DOI: 10.5808/gi.2017.15.1.19] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 12/15/2022] Open
Abstract
Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.
Collapse
Affiliation(s)
- Byoung-Ha Yoon
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seon-Kyu Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34113, Korea
| |
Collapse
|
241
|
Savarraj JPJ, Parsha K, Hergenroeder GW, Zhu L, Bajgur SS, Ahn S, Lee K, Chang T, Kim DH, Liu Y, Choi HA. Systematic model of peripheral inflammation after subarachnoid hemorrhage. Neurology 2017; 88:1535-1545. [PMID: 28314864 DOI: 10.1212/wnl.0000000000003842] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/16/2016] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To investigate inflammatory processes after aneurysmal subarachnoid hemorrhage (aSAH) with network models. METHODS This is a retrospective observational study of serum samples from 45 participants with aSAH analyzed at multiple predetermined time points: <24 hours, 24 to 48 hours, 3 to 5 days, and 6 to 8 days after aSAH. Concentrations of cytokines were measured with a 41-plex human immunoassay kit, and the Pearson correlation coefficients between all possible cytokine pairs were computed. Systematic network models were constructed on the basis of correlations between cytokine pairs for all participants and across injury severity. Trends of individual cytokines and correlations between them were examined simultaneously. RESULTS Network models revealed that systematic inflammatory activity peaks at 24 to 48 hours after the bleed. Individual cytokine levels changed significantly over time, exhibiting increasing, decreasing, and peaking trends. Platelet-derived growth factor (PDGF)-AA, PDGF-AB/BB, soluble CD40 ligand, and tumor necrosis factor-α (TNF-α) increased over time. Colony-stimulating factor (CSF) 3, interleukin (IL)-13, and FMS-like tyrosine kinase 3 ligand decreased over time. IL-6, IL-5, and IL-15 peaked and decreased. Some cytokines with insignificant trends show high correlations with other cytokines and vice versa. Many correlated cytokine clusters, including a platelet-derived factor cluster and an endothelial growth factor cluster, were observed at all times. Participants with higher clinical severity at admission had elevated levels of several proinflammatory and anti-inflammatory cytokines, including IL-6, CCL2, CCL11, CSF3, IL-8, IL-10, CX3CL1, and TNF-α, compared to those with lower clinical severity. CONCLUSIONS Combining reductionist and systematic techniques may lead to a better understanding of the underlying complexities of the inflammatory reaction after aSAH.
Collapse
Affiliation(s)
| | - Kaushik Parsha
- From the University of Texas Health Science Center at Houston
| | | | - Liang Zhu
- From the University of Texas Health Science Center at Houston
| | - Suhas S Bajgur
- From the University of Texas Health Science Center at Houston
| | - Sungho Ahn
- From the University of Texas Health Science Center at Houston
| | - Kiwon Lee
- From the University of Texas Health Science Center at Houston
| | - Tiffany Chang
- From the University of Texas Health Science Center at Houston
| | - Dong H Kim
- From the University of Texas Health Science Center at Houston
| | - Yin Liu
- From the University of Texas Health Science Center at Houston
| | - H Alex Choi
- From the University of Texas Health Science Center at Houston.
| |
Collapse
|
242
|
Reis VNDS, Kitajima JP, Tahira AC, Feio-dos-Santos AC, Fock RA, Lisboa BCG, Simões SN, Krepischi ACV, Rosenberg C, Lourenço NC, Passos-Bueno MR, Brentani H. Integrative Variation Analysis Reveals that a Complex Genotype May Specify Phenotype in Siblings with Syndromic Autism Spectrum Disorder. PLoS One 2017; 12:e0170386. [PMID: 28118382 PMCID: PMC5261619 DOI: 10.1371/journal.pone.0170386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/31/2016] [Indexed: 12/30/2022] Open
Abstract
It has been proposed that copy number variations (CNVs) are associated with increased risk of autism spectrum disorder (ASD) and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH) and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations—single nucleotide variants (SNVs) or small insertions and deletions (indels)—with probable functional impacts. With aCGH, we identified, in both siblings, a duplication in the 4p16.3 region and a deletion at 8p23.3, inherited by a paternal balanced translocation, t(4, 8) (p16; p23). Exome variant analysis found a total of 316 variants, of which 102 were shared by both siblings, 128 were in the male sibling exome data, and 86 were in the female exome data. Our integrative network analysis showed that the siblings’ shared translocation could explain their similar syndromic phenotype, including overgrowth, macrocephaly, and intellectual disability. However, exome data aggregate genes to those already connected from their translocation, which are important to the robustness of the network and contribute to the understanding of the broader spectrum of psychiatric symptoms. This study shows the importance of using an integrative approach to explore genotype-phenotype variability.
Collapse
MESH Headings
- Autism Spectrum Disorder/genetics
- Child
- Chromosomes, Human, Pair 4/genetics
- Chromosomes, Human, Pair 4/ultrastructure
- Chromosomes, Human, Pair 8/genetics
- Chromosomes, Human, Pair 8/ultrastructure
- Comparative Genomic Hybridization
- DNA Copy Number Variations
- Exome/genetics
- Female
- Gene Duplication
- Gene Regulatory Networks
- Genetic Association Studies
- Humans
- In Situ Hybridization, Fluorescence
- Intellectual Disability/genetics
- Learning Disabilities/genetics
- Male
- Megalencephaly/genetics
- Nerve Tissue Proteins/genetics
- Nucleic Acid Amplification Techniques
- Sequence Deletion
- Siblings
- Syndrome
- Translocation, Genetic
Collapse
Affiliation(s)
| | | | - Ana Carolina Tahira
- LIM23-Institute of Psychiatry, University of São Paulo School of Medicine, São Paulo, Brazil
| | | | - Rodrigo Ambrósio Fock
- Department of Morphology and Genetics, Federal University of São Paulo, São Paulo, Brazil
| | | | - Sérgio Nery Simões
- Department of Informatics, Federal Institute of Espírito Santo, Serra, Brazil
| | - Ana C. V. Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Naila Cristina Lourenço
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Helena Brentani
- LIM23-Institute of Psychiatry, University of São Paulo School of Medicine, São Paulo, Brazil
| |
Collapse
|
243
|
Nalluri JJ, Barh D, Azevedo V, Ghosh P. miRsig: a consensus-based network inference methodology to identify pan-cancer miRNA-miRNA interaction signatures. Sci Rep 2017; 7:39684. [PMID: 28045122 PMCID: PMC5206712 DOI: 10.1038/srep39684] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 11/25/2016] [Indexed: 01/17/2023] Open
Abstract
Decoding the patterns of miRNA regulation in diseases are important to properly realize its potential in diagnostic, prog- nostic, and therapeutic applications. Only a handful of studies computationally predict possible miRNA-miRNA interactions; hence, such interactions require a thorough investigation to understand their role in disease progression. In this paper, we design a novel computational pipeline to predict the common signature/core sets of miRNA-miRNA interactions for different diseases using network inference algorithms on the miRNA-disease expression profiles; the individual predictions of these algorithms were then merged using a consensus-based approach to predict miRNA-miRNA associations. We next selected the miRNA-miRNA associations across particular diseases to generate the corresponding disease-specific miRNA-interaction networks. Next, graph intersection analysis was performed on these networks for multiple diseases to identify the common signature/core sets of miRNA interactions. We applied this pipeline to identify the common signature of miRNA-miRNA inter- actions for cancers. The identified signatures when validated using a manual literature search from PubMed Central and the PhenomiR database, show strong relevance with the respective cancers, providing an indirect proof of the high accuracy of our methodology. We developed miRsig, an online tool for analysis and visualization of the disease-specific signature/core miRNA-miRNA interactions, available at: http://bnet.egr.vcu.edu/miRsig.
Collapse
Affiliation(s)
- Joseph J Nalluri
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, Virginia,USA
| | - Debmalya Barh
- Center for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, West Bengal, India.,Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil.,Xcode Life Sciences, 3D Eldorado, 112 Nungambakkam High Road, Nungambakkam, Chennai, Tamil Nadu-600034, India
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Preetam Ghosh
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, Virginia,USA
| |
Collapse
|
244
|
Chisanga D, Keerthikumar S, Mathivanan S, Chilamkurti N. Network Tools for the Analysis of Proteomic Data. Methods Mol Biol 2017; 1549:177-197. [PMID: 27975292 DOI: 10.1007/978-1-4939-6740-7_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recent advancements in high-throughput technologies such as mass spectrometry have led to an increase in the rate at which data is generated and accumulated. As a result, standard statistical methods no longer suffice as a way of analyzing such gigantic amounts of data. Network analysis, the evaluation of how nodes relate to one another, has over the years become an integral tool for analyzing high throughput proteomic data as they provide a structure that helps reduce the complexity of the underlying data.Computational tools, including pathway databases and network building tools, have therefore been developed to store, analyze, interpret, and learn from proteomics data. These tools enable the visualization of proteins as networks of signaling, regulatory, and biochemical interactions. In this chapter, we provide an overview of networks and network theory fundamentals for the analysis of proteomics data. We further provide an overview of interaction databases and network tools which are frequently used for analyzing proteomics data.
Collapse
Affiliation(s)
- David Chisanga
- Department of Computer Science and Information Technology, School of Engineering and Mathematical Sciencesy, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Naveen Chilamkurti
- Department of Computer Science and Information Technology, School of Engineering and Mathematical Sciencesy, La Trobe University, Melbourne, VIC, 3086, Australia.
| |
Collapse
|
245
|
Abstract
Functional relations between genes can be represented as networks. These networks have been successfully used to infer gene function and to mediate transfer of functional knowledge between species. Transcriptionally coordinated or co-expressed genes tend to be functionally related, which combined with availability of transcriptomic data for multiple plant species make the co-expression networks a useful resource for the plant community. In this chapter, we describe PlaNet ( www.gene2function.de ), a database that includes comparative analyses for co-expression networks of 11 plant species. We exemplify how the tools included in PlaNet can be used to predict gene function, transfer knowledge, and discover conserved and multiplied gene modules.
Collapse
Affiliation(s)
- Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| |
Collapse
|
246
|
Baghaei K, Hosseinkhan N, Asadzadeh Aghdaei H, Zali MR. Investigation of a common gene expression signature in gastrointestinal cancers using systems biology approaches. MOLECULAR BIOSYSTEMS 2017; 13:2277-2288. [DOI: 10.1039/c7mb00450h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
According to GLOBOCAN 2012, the incidence and the mortality rate of colorectal, stomach and liver cancers are the highest among the total gastrointestinal (GI) cancers.
Collapse
Affiliation(s)
- Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center
- Research Institute for Gastroenterology and Liver Diseases
- Shahid Beheshti University of Medical Sciences
- Tehran
- Iran
| | - Nazanin Hosseinkhan
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center
- Research Institute for Gastroenterology and Liver Diseases
- Shahid Beheshti University of Medical Sciences
- Tehran
- Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center
- Research Institute for Gastroenterology and Liver Diseases
- Shahid Beheshti University of Medical Sciences
- Tehran
- Iran
| | - M. R. Zali
- Gastroenterology and Liver Diseases Research Center
- Research Institute for Gastroenterology and Liver Diseases
- Shahid Beheshti University of Medical Sciences
- Tehran
- Iran
| |
Collapse
|
247
|
Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J. Efficient randomization of biological networks while preserving functional characterization of individual nodes. BMC Bioinformatics 2016; 17:542. [PMID: 27998275 PMCID: PMC5168876 DOI: 10.1186/s12859-016-1402-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 12/01/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and combinations of both. Additionally, a wide range of tools has been developed to map experimental data onto reference biological networks, in order to extract meaningful modules. Many of these methods assess results' significance against null distributions of randomized networks. However, these standard unconstrained randomizations do not preserve the functional characterization of the nodes in the reference networks (i.e. their degrees and connection signs), hence including potential biases in the assessment. RESULTS Building on our previous work about rewiring bipartite networks, we propose a method for rewiring any type of unweighted networks. In particular we formally demonstrate that the problem of rewiring a signed and directed network preserving its functional connectivity (F-rewiring) reduces to the problem of rewiring two induced bipartite networks. Additionally, we reformulate the lower bound to the iterations' number of the switching-algorithm to make it suitable for the F-rewiring of networks of any size. Finally, we present BiRewire3, an open-source Bioconductor package enabling the F-rewiring of any type of unweighted network. We illustrate its application to a case study about the identification of modules from gene expression data mapped on protein interaction networks, and a second one focused on building logic models from more complex signed-directed reference signaling networks and phosphoproteomic data. CONCLUSIONS BiRewire3 it is freely available at https://www.bioconductor.org/packages/BiRewire/ , and it should have a broad application as it allows an efficient and analytically derived statistical assessment of results from any network biology tool.
Collapse
Affiliation(s)
- Francesco Iorio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
| | - Marti Bernardo-Faura
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Andrea Gobbi
- Fondazione Bruno Kessler, Povo, Trento, I-38122, Italy
| | - Thomas Cokelaer
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | | | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK. .,RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), MTI2 Wendlingweg 2, Aachen, 52074, Germany.
| |
Collapse
|
248
|
Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C. STON: exploring biological pathways using the SBGN standard and graph databases. BMC Bioinformatics 2016; 17:494. [PMID: 27919219 PMCID: PMC5139139 DOI: 10.1186/s12859-016-1394-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/29/2016] [Indexed: 01/16/2023] Open
Abstract
Background When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks. Results We present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database. Conclusion STON exploits the power of graph databases to store and query complex biological pathways. This advances the possibility of: i) identifying subnetworks in a given pathway; ii) linking networks across different levels of granularity to address difficulties related to incomplete knowledge representation at single level; and iii) identifying common patterns between pathways in the database. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1394-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vasundra Touré
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051, Germany. .,European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France.
| | - Alexander Mazein
- European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France
| | - Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051, Germany
| | - Irina Balaur
- European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France
| | - Mansoor Saqi
- European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France
| | - Ron Henkel
- Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Department of Business Information Systems, University of Rostock, Rostock, 18051, Germany
| | - Johann Pellet
- European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France
| | - Charles Auffray
- European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France
| |
Collapse
|
249
|
Zhou Y. Small world properties changes in mild traumatic brain injury. J Magn Reson Imaging 2016; 46:518-527. [PMID: 27902865 DOI: 10.1002/jmri.25548] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022] Open
Abstract
PURPOSE To investigate local and global efficiency changes characterized by small-world properties based on resting-state functional MRI, such as centrality and clustering coefficient, in mild traumatic brain injury (MTBI) patients; and to associate these findings with axonal injury as measured by diffusion tensor imaging (DTI) as well as with post-concussive symptom (PCS). MATERIALS AND METHODS Thirty patients (mean age 35 ± 13 years) with clinically defined MTBI and 45 age-matched healthy controls (mean age 37 ± 10 years) participated in the experiments. Resting-state functional MRI was performed using gradient echo planar imaging sequence with 3 Tesla MRI scanner to obtain functional small-world networks. Out of all participants, 20 MTBI patients and 20 controls had available DTI data with three b-values (0, 500, 1000) s/mm2 and 30 directions for diffuse axonal injury analyses. RESULTS Compared with controls, MTBI patients showed lower relative betweenness centrality (P = 0.01), but significantly higher clustering coefficient (P = 0.04), and these two metrics correlated negatively in patients (r = -0.77; P < 0.001). Regions with lower betweenness centrality (e.g., frontal and occipital) corresponded with the regions of reduced FA in patients, while global FA reduction correlated with betweenness centrality (r = 0.48; P = 0.03) and clustering coefficient (r = -0.46; P = 0.04) in MTBI patients. In addition, there was significantly higher thalamocortical connectivity that correlated with clustering coefficient (r = 0.39; P = 0.03) in patients. Also, patients with higher clustering coefficient tended to have less PCS score with negative correlation (r = -0.4; P = 0.04). CONCLUSION Our results demonstrated significant functional small-world properties changes in patients with MTBI, and suggest decreased global efficiency, possibly due to diffuse axonal injury and local network upregulation including increased thalamo-cortical connectivity. LEVEL OF EVIDENCE 2 Technical Efficacy: Stage 2 J. MAGN. RESON. IMAGING 2017;46:518-527.
Collapse
Affiliation(s)
- Yongxia Zhou
- Department of Radiology / Center for Biomedical Imaging, NYU Langone Medical Center, New York, New York
| |
Collapse
|
250
|
Saeed MT, Ahmad J, Kanwal S, Holowatyj AN, Sheikh IA, Zafar Paracha R, Shafi A, Siddiqa A, Bibi Z, Khan M, Ali A. Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression. PeerJ 2016; 4:e2348. [PMID: 27703839 PMCID: PMC5047222 DOI: 10.7717/peerj.2348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022] Open
Abstract
The alteration of glucose metabolism, through increased uptake of glucose and glutamine addiction, is essential to cancer cell growth and invasion. Increased flux of glucose through the Hexosamine Biosynthetic Pathway (HBP) drives increased cellular O-GlcNAcylation (hyper-O-GlcNAcylation) and contributes to cancer progression by regulating key oncogenes. However, the association between hyper-O-GlcNAcylation and activation of these oncogenes remains poorly characterized. Here, we implement a qualitative modeling framework to analyze the role of the Biological Regulatory Network in HBP activation and its potential effects on key oncogenes. Experimental observations are encoded in a temporal language format and model checking is applied to infer the model parameters and qualitative model construction. Using this model, we discover step-wise genetic alterations that promote cancer development and invasion due to an increase in glycolytic flux, and reveal critical trajectories involved in cancer progression. We compute delay constraints to reveal important associations between the production and degradation rates of proteins. O-linked N-acetylglucosamine transferase (OGT), an enzyme used for addition of O-GlcNAc during O-GlcNAcylation, is identified as a key regulator to promote oncogenesis in a feedback mechanism through the stabilization of c-Myc. Silencing of the OGT and c-Myc loop decreases glycolytic flux and leads to programmed cell death. Results of network analyses also identify a significant cycle that highlights the role of p53-Mdm2 circuit oscillations in cancer recovery and homeostasis. Together, our findings suggest that the OGT and c-Myc feedback loop is critical in tumor progression, and targeting these mediators may provide a mechanism-based therapeutic approach to regulate hyper-O-GlcNAcylation in human cancer.
Collapse
Affiliation(s)
- Muhammad Tariq Saeed
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Jamil Ahmad
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan; School of Computer Science and IT, Stratford University, VA, United States
| | - Shahzina Kanwal
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou , China
| | - Andreana N Holowatyj
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute , Detroit , MI , United States
| | - Iftikhar A Sheikh
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Rehan Zafar Paracha
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Aamir Shafi
- School of Electrical Engineering and Computer Science (SEECS), National University of Sciences and Technology (NUST), Islamabad, Pakistan; College of Computer Science and Information Technology, University of Dammam, Al Khobar, Kingdom of Saudi Arabia
| | - Amnah Siddiqa
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Zurah Bibi
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Mukaram Khan
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Amjad Ali
- Atta-ur-Rehman School of Applied Bio-science (ASAB), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| |
Collapse
|