title: GECKO: a complete large-scale gene expression analysis platform.
abstract: BACKGROUND
  Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.
  
  
  RESULTS
  Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing approximately 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph), in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (approximately 100 users) and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data.
  
  
  CONCLUSIONS
  The Gecko system is being made publicly available as free software http://sourceforge.net/projects/geckoe. In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.
authors.affiliation: Cambridge Genomics Center, Sanofi-Aventis, 26 Landsdowne Street, Cambridge, MA 02139, USA. joachim.theilhaber@aventis.com
authors.forename: Joachim
authors.initials: J
authors.lastname: Theilhaber
authors.forename: Anatoly
authors.initials: A
authors.lastname: Ulyanov
authors.forename: Anish
authors.initials: A
authors.lastname: Malanthara
authors.forename: Jack
authors.initials: J
authors.lastname: Cole
authors.forename: Dapeng
authors.initials: D
authors.lastname: Xu
authors.forename: Robert
authors.initials: R
authors.lastname: Nahf
authors.forename: Michael
authors.initials: M
authors.lastname: Heuer
authors.forename: Christoph
authors.initials: C
authors.lastname: Brockel
authors.forename: Steven
authors.initials: S
authors.lastname: Bushnell
mesh_terms: D002277:Carcinoma / Q000145:classification / Q000235:genetics / Q000473:pathology; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D020869:Gene Expression Profiling / Q000145:classification / Q000379:methods* / Q000706:statistics & numerical data; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D052138:Genes, Neoplasm / Q000235:genetics; D006801:Humans; D007680:Kidney Neoplasms / Q000145:classification / Q000235:genetics / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis / Q000145:classification / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software; D012985:Software Design; D014584:User-Computer Interface