title: Screening and functional pathway analysis of genes associated with pediatric allergic asthma using a DNA microarray.
abstract: The present study aimed to identify differentially expressed genes (DEGs) associated with pediatric allergic asthma, and to analyze the functional pathways of the selected target genes, in order to explore the pathogenesis of the disease. The GSE18965 gene expression profile was downloaded from the Gene Expression Omnibus database and was preprocessed. This gene expression profile consisted of seven normal samples and nine samples from patients with pediatric allergic asthma. The DEGs between the normal and pediatric allergic asthma samples were screened using limma package in R, and the cut‑off value was set at false discovery rate <0.05 and log fold change >1. Following hierarchical clustering of the DEGs based on the expression profiles, the up‑ and downregulated genes underwent a functional enrichment analysis by topological approach (P<0.05), using the Database for Annotation, Visualization and Integrated Discovery. A total of 127 DEGs were identified between the normal and pediatric allergic asthma samples. The up‑ and downregulated genes were significantly enriched in the actin filament‑based process and the monosaccharide metabolic process, respectively. Seven downregulated DEGs (M6PR, TPP1, GLB1, NEU1, ACP2, LAMP1 and HGSNAT) were identified in the lysosomal pathway, with P=6.4x10(‑9). These results suggested that variation in lysosomal function, triggered by the seven downregulated genes, may lead to aberrant functioning of the T lymphocytes, resulting in asthma. Further research regarding the treatment of pediatric allergic asthma through targeting lysosomal function is required.
authors: Department of Pediatrics, First Hospital Affiliated to Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China.
authors: Li-Qun
authors: LQ
authors: Lu
authors: Department of Pediatrics, Southwest Hospital, The Third Military Medical University, Chongqing 400038, P.R. China.
authors: Wei
authors: W
authors: Liao
mesh_terms: D000367:Age Factors; D001249:Asthma / Q000235:genetics* / Q000378:metabolism*; D002648:Child; D016000:Cluster Analysis; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D008297:Male; D058977:Molecular Sequence Annotation; D015398:Signal Transduction; D000091346:Tripeptidyl-Peptidase 1
references: BMC Bioinformatics. 2006;7:469
references: 17059609
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7
references: 16381885
references: BMC Genomics. 2007;8:214
references: 17610740
references: Am J Hum Genet. 2006 Oct;79(4):738-44
references: 16960811
references: MMWR Surveill Summ. 2002 Mar 29;51(1):1-13
references: 12420904
references: Mol Aspects Med. 2006 Oct-Dec;27(5-6):495-502
references: 16973206
references: J Allergy Clin Immunol. 2005 Feb;115(2):213-9; quiz 220
references: 15696070
references: Chest. 1993 May;103(5):1316-7
references: 8486001
references: Hum Mutat. 2005 Mar;25(3):285-92
references: 15714521
references: Eur Rev Med Pharmacol Sci. 2012 Dec;16(14):1961-6
references: 23242723
references: J Med Genet. 2004 Dec;41(12):941-5
references: 15591281
references: Am J Physiol Lung Cell Mol Physiol. 2009 Feb;296(2):L185-97
references: 19028979
references: Int Immunopharmacol. 2012 Mar;12(3):518-25
references: 22293534
references: Nat Rev Genet. 2010 Mar;11(3):191-203
references: 20125086
references: Annu Rev Biomed Eng. 2002;4:129-53
references: 12117754
references: Nucleic Acids Res. 2009 Jan;37(1):1-13
references: 19033363
references: Tohoku J Exp Med. 2005 Oct;207(2):109-18
references: 16141679
references: BMC Bioinformatics. 2007;8:460
references: 18034891
references: Trends Cell Biol. 2003 Mar;13(3):137-45
references: 12628346
references: Multidiscip Respir Med. 2013 Feb 11;8(1):12
references: 23398734
references: Eur Rev Med Pharmacol Sci. 2012 Jul;16(7):867-72
references: 22953633
references: J Allergy Clin Immunol. 2001 Jan;107(1):171-7
references: 11150008
references: J Cell Sci. 2000 May;113 ( Pt 9):1515-24
references: 10751143
references: BMC Genomics. 2011;12:12
references: 21211037
references: Pulm Med. 2012;2012:834826
references: 22966430
references: J Allergy Clin Immunol. 2012 Apr;129(4):1020-30
references: 22464673
references: Birth Defects Res B Dev Reprod Toxicol. 2008 Dec;83(6):547-60
references: 19085948
references: Am J Respir Crit Care Med. 2010 May 1;181(9):889-98
references: 20110557
references: Ann Allergy Asthma Immunol. 1997 Sep;79(3):177-85; quiz 185-6
references: 9305223
references: Intern Med. 2003 Aug;42(8):636-43
references: 12924484
references: Nat Protoc. 2009;4(1):44-57
references: 19131956
references: BMC Bioinformatics. 2004 Sep 1;5:120
references: 15339344
references: J Allergy Clin Immunol. 1996 Dec;98(6 Pt 1):1051-7
references: 8977504
references: Nature. 2000 Aug 24;406(6798):902-6
references: 10972293