Journal ArticleDOI
Multiple Gene Expression Dataset Analysis Reveals Toll-Like Receptor Signaling Pathway is Strongly Associated With Chronic Obstructive Pulmonary Disease Pathogenesis
TLDR
CXCL9, CXCL10, C XCL11, CCL4, TLR7, and SPP1 hub genes in the toll-like receptor signaling pathway were explored in this study as potential biomarker genes associated with COPD pathogenesis.Abstract:
Chronic obstructive pulmonary disease is a complex pulmonary disease that causes airflow obstruction in humans. To identify the core genes in COPD pathogenesis, seven diverse microarray datasets (GSE475, GSE1122, GSE1650, GSE3212, GSE8823, GSE37768, and GSE22148) were downloaded from the gene expression omnibus database. All the datasets were analyzed independently with the R/Bioconductor package to screen the differentially expressed genes (DEGs). The gene ontology and pathway enrichment analysis were performed for the acquired DEGs using DAVID (Database for Annotation, Visualization, and Integrated Discovery). Further protein-protein interaction network was constructed for the DEGs and their potential hub genes and sub-networks were identified using Cytoscape software. From the selected seven datasets, 188 overlapped DEGs were perceived eventually based on considering the repetitive genes between at-least one dataset. Gene Ontology analysis reveals that most of the DEGs were significantly enriched in immune response, inflammatory response, extracellular region, lipid binding, cytokine, and chemokine activity. Moreover, genes from the sub-network analysis were again submitted to the DAVID server to validate the results which uncover the Toll-like receptor signaling pathway was significantly enriched and all the genes present in this pathway were likewise detected as hub genes from Cytoscape software. CXCL9, CXCL10, CXCL11, CCL4, TLR7, and SPP1 hub genes in the toll-like receptor signaling pathway were explored in this study as potential biomarker genes associated with COPD pathogenesis.read more
Citations
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Journal ArticleDOI
Identification of Inflammation-Related Biomarker Lp-PLA2 for Patients With COPD by Comprehensive Analysis
TL;DR: Wang et al. as discussed by the authors used differential expressed genes analysis and weighted co-expression network analysis to explore potential biomarker Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene set enrichment analysis (GSEA) analysis were used to explore the potential mechanism CIBERSORTx website was used to evaluate tissue-infiltrating immune cells.
Posted ContentDOI
Identification of COVID-19 and COPD common key genes and pathways using a protein-protein interaction approach
TL;DR: In this article, a network of protein-protein interaction (PPI) was developed using constructed datasets of COVID-19 and COPD genes to define the interrelationship between COVID19 and chronic obstructive pulmonary disease, how it affects each other, and the genes that are responsible for the process.
References
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Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
Journal ArticleDOI
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
TL;DR: The survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
Journal ArticleDOI
Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010
Rafael Lozano,Mohsen Naghavi,Kyle J Foreman,Stephen S Lim,Kenji Shibuya,Victor Aboyans,Jerry Abraham,Tim Adair,Rakesh Aggarwal,Stephanie Y. Ahn,Mohammad A. AlMazroa,Miriam Alvarado,H. Ross Anderson,Laurie M. Anderson,Kathryn G. Andrews,Charles Atkinson,Larry M. Baddour,Suzanne Barker-Collo,David Bartels,Michelle L. Bell,Emelia J. Benjamin,Derrick A Bennett,Kavi Bhalla,Boris Bikbov,Aref A. Bin Abdulhak,Gretchen L. Birbeck,Fiona M. Blyth,Ian Bolliger,Soufiane Boufous,Chiara Bucello,Michael Burch,Peter Burney,Jonathan R. Carapetis,Honglei Chen,David Chou,Sumeet S. Chugh,Luc E. Coffeng,Steven D. Colan,Samantha M. Colquhoun,K. Ellicott Colson,John R. Condon,Myles Connor,Myles Connor,Leslie T. Cooper,Matthew A. Corriere,Monica Cortinovis,Karen Courville De Vaccaro,William G. Couser,Benjamin C Cowie,Michael H. Criqui,Marita Cross,Kaustubh Dabhadkar,Nabila Dahodwala,Diego De Leo,Louisa Degenhardt,Allyne Delossantos,Julie O. Denenberg,Don C. Des Jarlais,Samath D Dharmaratne,Samath D Dharmaratne,E. Ray Dorsey,Tim Driscoll,Herbert C. Duber,Beth E. Ebel,Patricia J. Erwin,Patricia Espindola,Majid Ezzati,Valery L. Feigin,Abraham D. Flaxman,Mohammad H. Forouzanfar,F.G.R. Fowkes,Richard C. Franklin,Marlene Fransen,Michael Freeman,Sherine E. Gabriel,Emmanuela Gakidou,Flavio Gaspari,Richard F. Gillum,Diego Gonzalez-Medina,Yara A. Halasa,Diana Haring,James Harrison,Rasmus Havmoeller,Rasmus Havmoeller,Roderick J. Hay,Bruno Hoen,Peter J. Hotez,Damian G Hoy,Kathryn H. Jacobsen,Spencer L. James,Rashmi Jasrasaria,Sudha Jayaraman,Nicole E. Johns,Ganesan Karthikeyan,Nicholas J Kassebaum,Andre Keren,Jon Paul Khoo,Lisa M. Knowlton,Olive Kobusingye,Adofo Koranteng,Rita Krishnamurthi,Michael S Lipnick,Steven E. Lipshultz,Summer Lockett Ohno,Jacqueline Mabweijano,Jacqueline Mabweijano,Michael F. Macintyre,Leslie Mallinger,Lyn March,Guy B. Marks,Robin Marks,Akira Matsumori,Richard Matzopoulos,Richard Matzopoulos,Bongani M. Mayosi,John H. McAnulty,Mary M. McDermott,John J. McGrath,Ziad A. Memish,George A. Mensah,Tony R. Merriman,Catherine Michaud,Matthew J. Miller,Ted R. Miller,Charles Mock,Ana Olga Mocumbi,Ali A. Mokdad,Andrew E. Moran,Kim Mulholland,M. Nathan Nair,Luigi Naldi,K.M. Venkat Narayan,Kiumarss Nasseri,Paul Norman,Martin O'Donnell,Saad B. Omer,Katrina F Ortblad,Richard H. Osborne,Doruk Ozgediz,Bishnu Pahari,Jeyaraj D Pandian,Andrea Panozo Rivero,Rogelio Perez Padilla,Fernando Perez-Ruiz,Norberto Perico,David Phillips,Kelsey Pierce,C. Arden Pope,Esteban Porrini,Farshad Pourmalek,Murugesan Raju,Dharani Ranganathan,Jürgen Rehm,David B. Rein,G. Remuzzi,Frederick P. Rivara,Thomas Roberts,Felipe Rodriguez De Leòn,Lisa C. Rosenfeld,Lesley Rushton,Ralph L. Sacco,Joshua A. Salomon,Uchechukwu Sampson,Ella Sanman,David C. Schwebel,Maria Segui-Gomez,Donald S. Shepard,David Singh,Jessica Singleton,Karen Sliwa,Emma Smith,Andrew C Steer,Jennifer A. Taylor,Bernadette Thomas,Imad M. Tleyjeh,Jeffrey A. Towbin,Thomas Truelsen,Eduardo A. Undurraga,Narayanaswamy Venketasubramanian,Lakshmi Vijayakumar,Theo Vos,Gregory R. Wagner,Mengru Wang,Wenzhi Wang,Kerrianne Watt,Martin A. Weinstock,Robert G. Weintraub,James D. Wilkinson,Anthony D. Woolf,Sarah Wulf,Pon Hsiu Yeh,Paul S. F. Yip,Azadeh Zabetian,Zhi Jie Zheng,Alan D. Lopez,Christopher J L Murray +195 more
TL;DR: The Global Burden of Diseases, Injuries, and Risk Factors Study 2010 aimed to estimate annual deaths for the world and 21 regions between 1980 and 2010 for 235 causes, with uncertainty intervals (UIs), separately by age and sex, using the Cause of Death Ensemble model.
Journal ArticleDOI
Toll-like receptor signalling
Shizuo Akira,Kiyoshi Takeda +1 more
TL;DR: Rapid progress that has recently improved the understanding of the molecular mechanisms that mediate TLR signalling is reviewed.