GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.
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.
Yu
Yao
Y
Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China. yyu01@sibs.ac.cn
Tu
Kang
K
Zheng
Siyuan
S
Li
Yun
Y
Ding
Guohui
G
Ping
Jie
J
Hao
Pei
P
Li
Yixue
Y
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015870:Gene Expression; D010641:Phenotype; D012984:Software; D014584:User-Computer Interface
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