GECKO: a complete large-scale gene expression analysis platform.
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.
Theilhaber
Joachim
J
Cambridge Genomics Center, Sanofi-Aventis, 26 Landsdowne Street, Cambridge, MA 02139, USA. joachim.theilhaber@aventis.com
Ulyanov
Anatoly
A
Malanthara
Anish
A
Cole
Jack
J
Xu
Dapeng
D
Nahf
Robert
R
Heuer
Michael
M
Brockel
Christoph
C
Bushnell
Steven
S
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