title: GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.
abstract: BACKGROUND
  In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and analyzing in scientific researches.
  
  
  RESULTS
  In our work, we integrated gene expression information from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis - GEOGLE. GEOGLE offers a rapid and convenient way for searching relevant experimental datasets, pathways and biological terms according to multiple types of queries: including biomedical vocabularies, GDS IDs, gene IDs, pathway names and signature list. Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value.
  
  
  CONCLUSIONS
  This approach performing global searching of expression data may expand the traditional way of collecting heterogeneous gene expression experiment data. GEOGLE is a novel tool that provides researchers a quantitative way to understand the correlation between gene expression and phenotypic distinction through meta-analysis of gene expression datasets from different experiments, as well as the biological meaning behind. The web site and user guide of GEOGLE are available at: http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020.
authors.affiliation: Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China. yyu01@sibs.ac.cn
authors.forename: Yao
authors.initials: Y
authors.lastname: Yu
authors.forename: Kang
authors.initials: K
authors.lastname: Tu
authors.forename: Siyuan
authors.initials: S
authors.lastname: Zheng
authors.forename: Yun
authors.initials: Y
authors.lastname: Li
authors.forename: Guohui
authors.initials: G
authors.lastname: Ding
authors.forename: Jie
authors.initials: J
authors.lastname: Ping
authors.forename: Pei
authors.initials: P
authors.lastname: Hao
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015870:Gene Expression; D010641:Phenotype; D012984:Software; D014584:User-Computer Interface
references.citation: Cancer Res. 2002 Aug 1;62(15):4427-33
references.pmid: 12154050
references.citation: Nat Rev Cancer. 2007 Jan;7(1):54-60
references.pmid: 17186018
references.citation: Genome Biol. 2007;8(7):R133
references.pmid: 17612401
references.citation: Cancer Epidemiol Biomarkers Prev. 2008 Feb;17(2):397-404
references.pmid: 18268124
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W741-8
references.pmid: 15980575
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D766-70
references.pmid: 17182626
references.citation: Methods Enzymol. 2006;411:352-69
references.pmid: 16939800
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W308-14
references.pmid: 18508806
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W457-9
references.pmid: 15215429
references.citation: Bioinformatics. 2007 Jul 15;23(14):1846-7
references.pmid: 17496320
references.citation: Bioinformatics. 2008 Apr 15;24(8):1102-3
references.pmid: 18353790
references.citation: N Engl J Med. 2002 Dec 19;347(25):1999-2009
references.pmid: 12490681
references.citation: C R Biol. 2003 Oct-Nov;326(10-11):1075-8
references.pmid: 14744115
references.citation: Bioinformatics. 2008 Oct 15;24(20):2412-3
references.pmid: 18697766
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W341-6
references.pmid: 18515841
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):207-10
references.pmid: 11752295
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D880-4
references.pmid: 19073704
references.citation: Neoplasia. 2007 Feb;9(2):166-80
references.pmid: 17356713
references.citation: J Clin Invest. 2005 Jun;115(6):1503-21
references.pmid: 15931389
references.citation: Am J Respir Cell Mol Biol. 2006 Sep;35(3):327-36
references.pmid: 16614352
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 22;101(25):9309-14
references.pmid: 15184677
references.citation: Bioinformatics. 2005 May 15;21(10):2550-1
references.pmid: 15746290
references.citation: BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S56
references.pmid: 19208159
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13544-9
references.pmid: 16174746
references.citation: Neoplasia. 2004 Jan-Feb;6(1):1-6
references.pmid: 15068665
references.citation: JAMA. 1994 Apr 13;271(14):1103-8
references.pmid: 8151853
references.citation: PLoS One. 2008;3(12):e3863
references.pmid: 19057651
references.citation: Methods Mol Biol. 2006;338:175-90
references.pmid: 16888359
references.citation: BMC Bioinformatics. 2008 Dec 22;9:552
references.pmid: 19099609