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Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. Biophysics (Nagoya-shi) 2019; 63:43-51. [PMID: 30739944 DOI: 10.1134/s0006350918010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene regulatory networks control the complex programs that drive development. Deciphering the connections between transcription factors (TFs) and target genes is challenging, in part because TFs bind to thousands of places in the genome but control expression through a subset of these binding events. We hypothesize that we can combine natural variation of expression levels and predictions of TF binding sites to identify TF targets. We gather RNA-seq data from 71 genetically distinct F1 Drosophila melanogaster embryos and calculate the correlations between TF and potential target genes' expression levels, which we call "regulatory strength." To separate direct and indirect TF targets, we hypothesize that direct TF targets will have a preponderance of binding sites in their upstream regions. Using 14 TFs active during embryogenesis, we find that 12 TFs showed a significant correlation between their binding strength and regulatory strength on downstream targets, and 10 TFs showed a significant correlation between the number of binding sites and the regulatory effect on target genes. The general roles, e.g. bicoid's role as an activator, and the particular interactions we observed between our TFs, e.g. twist's role as a repressor of sloppy paired and odd paired, generally coincide with the literature.
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Affiliation(s)
- Noha M Osman
- University of Southern California, Los Angeles, CA.,National Research Centre, Dokki, Giza, Egypt
| | | | - Srna Vlaho
- University of Southern California, Los Angeles, CA
| | | | - Sergey V Nuzhdin
- University of Southern California, Los Angeles, CA.,Saint Petersburg Polytechnical University, St Petersburg, Russia
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2
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Te Pas MFW, Madsen O, Calus MPL, Smits MA. The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype. Int J Mol Sci 2017; 18:E472. [PMID: 28241430 PMCID: PMC5344004 DOI: 10.3390/ijms18020472] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 02/06/2023] Open
Abstract
With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals' microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.
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Affiliation(s)
- Marinus F W Te Pas
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University, 6700AH Wageningen, The Netherlands.
| | - Mario P L Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
| | - Mari A Smits
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
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3
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Abstract
Interactions among biological entities contain more information than purely the similarities between the entities. For example, interactions between genes, and gene products, can be more informative than the sequence similarities of the genes involved. However, the study of biological networks and their evolution in particular is still in its infancy. Simplified theoretical models of the development of biological networks from a starting state exist, but the problem of finding a distance between existing biological networks, with an unknown history, has seen less research. Metrics for network distance can also be used to measure the fit between theoretically derived networks and their real-world counterpart. In this article, we present a useful model of biological network distance and demonstrate an implementation using simulated gene regulatory networks. We compared our method with existing methods for network alignment and showed that we are much better able to identify evolutionary changes in biological networks. In particular, we can recover the evolutionary trees that describe the relationship between these networks.
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Affiliation(s)
- Martin McGrane
- 1 School of Information Technologies, The University of Sydney , Sydney, New South Wales, Australia
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4
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Lee KJ, Yin W, Arafat D, Tang Y, Uppal K, Tran V, Cabrera-Mora M, Lapp S, Moreno A, Meyer E, DeBarry JD, Pakala S, Nayak V, Kissinger JC, Jones DP, Galinski M, Styczynski MP, Gibson G. Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. Front Cell Dev Biol 2014; 2:54. [PMID: 25453034 PMCID: PMC4233942 DOI: 10.3389/fcell.2014.00054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/08/2014] [Indexed: 01/02/2023] Open
Abstract
We describe a multi-omic approach to understanding the effects that the anti-malarial drug pyrimethamine has on immune physiology in rhesus macaques (Macaca mulatta). Whole blood and bone marrow (BM) RNA-Seq and plasma metabolome profiles (each with over 15,000 features) have been generated for five naïve individuals at up to seven timepoints before, during and after three rounds of drug administration. Linear modeling and Bayesian network analyses are both considered, alongside investigations of the impact of statistical modeling strategies on biological inference. Individual macaques were found to be a major source of variance for both omic data types, and factoring individuals into subsequent modeling increases power to detect temporal effects. A major component of the whole blood transcriptome follows the BM with a time-delay, while other components of variation are unique to each compartment. We demonstrate that pyrimethamine administration does impact both compartments throughout the experiment, but very limited perturbation of transcript or metabolite abundance was observed following each round of drug exposure. New insights into the mode of action of the drug are presented in the context of pyrimethamine's predicted effect on suppression of cell division and metabolism in the immune system.
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Affiliation(s)
- Kevin J Lee
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Weiwei Yin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta, GA, USA
| | - Dalia Arafat
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Yan Tang
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, Emory University Atlanta, GA, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, Emory University Atlanta, GA, USA
| | - Monica Cabrera-Mora
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA
| | - Stacey Lapp
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA
| | - Alberto Moreno
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA ; Division of Infectious Diseases, Department of Medicine, Emory University Atlanta, GA, USA
| | - Esmeralda Meyer
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA
| | - Jeremy D DeBarry
- Center for Topical and Emerging Global Diseases, University of Georgia Athens, GA, USA
| | - Suman Pakala
- Institute of Bioinformatics, University of Georgia Athens, GA, USA
| | - Vishal Nayak
- Institute of Bioinformatics, University of Georgia Athens, GA, USA
| | - Jessica C Kissinger
- Center for Topical and Emerging Global Diseases, University of Georgia Athens, GA, USA ; Institute of Bioinformatics, University of Georgia Athens, GA, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, Emory University Atlanta, GA, USA
| | - Mary Galinski
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University Atlanta, GA, USA ; Division of Infectious Diseases, Department of Medicine, Emory University Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta, GA, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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5
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Abstract
Integrative genomics studies have greatly advanced our understanding of cardiovascular pathophysiology over the last decade. Here, we highlight the strengths and challenges of this cutting-edge approach and provide examples where novel insights have arisen through the integration of multi-level genomic information and cardiac physiology. Going forward, the integration of comprehensive next-generation sequencing data sets with quantitative phenotypes at the molecular, cellular, and whole-heart level using advanced modelling approaches provides an unprecedented opportunity for cardiovascular science.
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Affiliation(s)
- James S Ware
- MRC Clinical Sciences Centre, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
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6
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Wright FA, Shabalin AA, Rusyn I. Computational tools for discovery and interpretation of expression quantitative trait loci. Pharmacogenomics 2012; 13:343-52. [PMID: 22304583 DOI: 10.2217/pgs.11.185] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Expression quantitative trait locus (eQTL) analysis is rapidly moving from a cutting-edge concept in genomics to a mature area of investigation, with important connections to genome-wide association studies for human disease, pharmacogenomics and toxicogenomics. Despite the importance of the topic, many investigators must develop their own code or use tools not specifically suited for eQTL analysis. Convenient computational tools are becoming available, but they are not widely publicized, and investigators who are interested in discovery or eQTL, or in using them to interpret genome-wide association study results may have difficulty navigating the available resources. The purpose of this review is to help investigators find appropriate programs for eQTL analysis and interpretation.
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Affiliation(s)
- Fred A Wright
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
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7
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Freedman ML, Monteiro ANA, Gayther SA, Coetzee GA, Risch A, Plass C, Casey G, De Biasi M, Carlson C, Duggan D, James M, Liu P, Tichelaar JW, Vikis HG, You M, Mills IG. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 2011; 43:513-8. [PMID: 21614091 PMCID: PMC3325768 DOI: 10.1038/ng.840] [Citation(s) in RCA: 325] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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8
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Gatti DM, Lu L, Williams RW, Sun W, Wright FA, Threadgill DW, Rusyn I. MicroRNA expression in the livers of inbred mice. Mutat Res 2011; 714:126-33. [PMID: 21616085 DOI: 10.1016/j.mrfmmm.2011.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 05/05/2011] [Accepted: 05/08/2011] [Indexed: 01/07/2023]
Abstract
MicroRNAs are short, non-coding RNA sequences that regulate genes at the post-transcriptional level and have been shown to be important in development, tissue differentiation, and disease. Limited attention has been given to the natural variation in miRNA expression across genetically diverse populations even though it is well established that genetic polymorphisms can have a profound effect on mRNA levels. Expression level of 577 miRNAs in the livers of 70 strains of inbred mice was assessed, and we found that miRNA expression is highly stable across different strains. Globally, the expression of miRNA target transcripts does not correlate with miRNA expression, primarily due to the low variance of miRNA but high variance of mRNA expression across strains. Our results show that there is little genetic effect on the baseline miRNA levels in murine liver. The stability of mouse liver miRNA expression in a genetically diverse population suggests that treatment-induced disruptions in liver miRNA expression, a phenomenon established for a large number of toxicants, may indicate an important mechanism for the disturbance of normal liver function, and may prove to be a useful genetic background-independent biomarker of toxicant effect.
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Affiliation(s)
- Daniel M Gatti
- Department of Environmental Sciences & Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
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9
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Abstract
Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology.
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Affiliation(s)
- Mikaël Lucas
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, UK.
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10
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Sucaet Y, Deva T. Evolution and applications of plant pathway resources and databases. Brief Bioinform 2011; 12:530-44. [PMID: 21949268 DOI: 10.1093/bib/bbq083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plants are important sources of food and plant products are essential for modern human life. Plants are increasingly gaining importance as drug and fuel resources, bioremediation tools and as tools for recombinant technology. Considering these applications, database infrastructure for plant model systems deserves much more attention. Study of plant biological pathways, the interconnection between these pathways and plant systems biology on the whole has in general lagged behind human systems biology. In this article we review plant pathway databases and the resources that are currently available. We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration. We also discuss how progress in non-plant communities can serve as an example for the improvement of the plant pathway database landscape and thereby allow quantitative modeling of plant biosystems. We propose Good Database Practice as a possible model for collaboration and to ease future integration efforts.
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11
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Repetitive peroxide exposure reveals pleiotropic mitogen-activated protein kinase signaling mechanisms. JOURNAL OF SIGNAL TRANSDUCTION 2010; 2011:636951. [PMID: 21258655 PMCID: PMC3023409 DOI: 10.1155/2011/636951] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 09/28/2010] [Indexed: 01/14/2023]
Abstract
Oxidative stressors such as hydrogen peroxide control the activation of many interconnected signaling systems and are implicated in neurodegenerative disease etiology. Application of hydrogen peroxide to PC12 cells activated multiple tyrosine kinases (c-Src, epidermal growth factor receptor (EGFR), and Pyk2) and the serine-threonine kinase ERK1/2. Peroxide-induced ERK1/2 activation was sensitive to intracellular calcium chelation and EGFR and c-Src kinase inhibition. Acute application and removal of peroxide allowed ERK1/2 activity levels to rapidly subside to basal serum-deprived levels. Using this protocol, we demonstrated that ERK1/2 activation tachyphylaxis developed upon repeated peroxide exposures. This tachyphylaxis was independent of c-Src/Pyk2 tyrosine phosphorylation but was associated with a progressive reduction of peroxide-induced EGFR tyrosine phosphorylation, EGFR interaction with growth factor receptor binding protein 2, and a redistribution of EGFR from the plasma membrane to the cytoplasm. Our data indicates that components of peroxide-induced ERK1/2 cascades are differentially affected by repeated exposures, indicating that oxidative signaling may be contextually variable.
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12
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Abstract
Environmental stressors such as chemicals and physical agents induce various oxidative stresses and affect human health. To elucidate their underlying mechanisms, etiology and risk, analyses of gene expression signatures in environmental stress-induced human diseases, including neuronal disorders, cancer and diabetes, are crucially important. Recent studies have clarified oxidative stress-induced signaling pathways in human and experimental animals. These pathways are classifiable into several categories: reactive oxygen species (ROS) metabolism and antioxidant defenses, p53 pathway signaling, nitric oxide (NO) signaling pathway, hypoxia signaling, transforming growth factor (TGF)-beta bone morphogenetic protein (BMP) signaling, tumor necrosis factor (TNF) ligand-receptor signaling, and mitochondrial function. This review describes the gene expression signatures through which environmental stressors induce oxidative stress and regulate signal transduction pathways in rodent and human tissues.
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Affiliation(s)
- H Sone
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan.
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13
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Przytycka TM, Singh M, Slonim DK. Toward the dynamic interactome: it's about time. Brief Bioinform 2010; 11:15-29. [PMID: 20061351 PMCID: PMC2810115 DOI: 10.1093/bib/bbp057] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 11/01/2009] [Indexed: 11/14/2022] Open
Abstract
Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms. The availability of experimentally determined large-scale cellular networks, along with other high-throughput experimental data sets that provide snapshots of biological systems at different times and conditions, is increasingly helpful in elucidating interaction dynamics. Here we review the beginnings of a new subfield within computational biology, one focused on the global inference and analysis of the dynamic interactome. This burgeoning research area, which entails a shift from static to dynamic network analysis, promises to be a major step forward in our ability to model and reason about cellular function and behavior.
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Affiliation(s)
- Teresa M Przytycka
- National Center of Biotechnology Information, NLM, NIH, 8000 Rockville Pike, Bethesda MD 20814, USA.
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14
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Diez D, Wheelock AM, Goto S, Haeggström JZ, Paulsson-Berne G, Hansson GK, Hedin U, Gabrielsen A, Wheelock CE. The use of network analyses for elucidating mechanisms in cardiovascular disease. MOLECULAR BIOSYSTEMS 2009; 6:289-304. [PMID: 20094647 DOI: 10.1039/b912078e] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Systems biology offers the potential to provide new insights into our understanding of the pathogenesis of complex diseases such as atherosclerosis. It seeks to comprehend the system properties of the non-linear interactions of the multiple biomolecular components that characterize a living organism. An important component of this research approach is identifying the biological networks that connect the differing elements of a system and in the process describe the characteristics that define a shift in equilibrium from a healthy to a diseased state. The utility of this method becomes clear when applied to multifactorial diseases with complex etiologies such as inflammatory-related diseases, herein exemplified by cardiovascular disease. In this study, the application of network theory to systems biology is described in detail and an example is provided using data from a clinical biobank database of carotid endarterectomies from the Karolinska University Hospital (Biobank of Karolinska Endarterectomies, BiKE). Data from 47 microarrays were examined using a combination of Bioconductor modules and the Cytoscape resource with several associated plugins to analyze the transcriptomics data and create a combined gene association and correlation network of atherosclerosis. The methodology and workflow are described in detail, with a total of 43 genes found to be differentially expressed on a gender-specific basis, of which 15 were not directly linked to the sex chromosomes. In particular, the APOC1 gene was 2.1-fold down-regulated in plaques in women relative to men and was selected for further analysis based upon a purported role in cardiovascular disease. The resulting network was identified as a scale-free network that contained specific sub-networks related to immune function and lipid biosynthesis. These sub-networks link atherosclerotic-related genes to other genes that may not have previously known roles in disease etiology and only evidence small alterations, which are challenging to find by statistical and comparison-based methods. A number of Gene Ontology (GO), BioCarta and KEGG pathways involved in the atherosclerotic process were identified in the constructed sub-network, with 19 GO pathways related to APOC1 of which 'phospholipid efflux' evidenced the strongest association. The utility and functionality of network analysis and the different Cytoscape plugins employed are discussed. Lastly, the applications of these methods to cardiovascular disease are discussed with focus on the current limitations and future visions of this emerging field.
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Affiliation(s)
- Diego Diez
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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