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A Database of Heterogeneous Gene Expression Data Based on A Consistent Gene Nomenclature

Tutorial and training materials by OpenHelix

Learn to use CleanEx, an online database of genome-wide gene expression data. In CleanEx users can access human and mouse expression data by approved gene symbols, or by searching with MeSH terms for experiments representing specific biological conditions. Expression data are presented in such a way that they can be compared to each other even if they were obtained using different methods. The CleanEx Target database contains sequence and quality information on microarray probes and sequence tags associated with a gene. The resource also includes data analysis tools for identification of over- or underexpressed genes. If your research involves gene expression data, then learn to use CleanEx to help facilitate data analysis.

You'll learn:

  • to find information on transcript abundance and expression targets by gene names
  • to extract numerical expression data from CleanEx
  • to search for datasets or subsets representing biological conditions of interest, using MeSH terms
  • to identify over- or underexpressed genes in a dataset, and examine the expression pattern of these genes in other datasets
  • to identify genes whose expression levels correlate with a biological condition across multiple datasets


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Recent BioMed Central research articles citing this resource

Glaser Johann et al., FACET – a “Flexible Artifact Correction and Evaluation Toolbox” for concurrently recorded EEG/fMRI data Computational and theoretical neuromodeling. BMC Neuroscience (2013) doi:10.1186/1471-2202-14-138

Kaur Mandeep et al., In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. BMC Systems Biology (2011) doi:10.1186/1752-0509-5-144

Cheng Wei-Chung et al., Microarray meta-analysis database (M 2 DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC Bioinformatics (2010) doi:10.1186/1471-2105-11-421

Guffanti Alessandro et al., A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics (2009) doi:10.1186/1471-2164-10-163

Yu Yao et al., GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics (2009) doi:10.1186/1471-2105-10-264

More about the resource:

CleanEx was developed by scientists at the Computational Cancer Genomics group at the Swiss Institute of Bioinformatics, or SIB. It imports publicly available human and mouse gene expression data, generated by microarray technology and sequencing-based methods. CleanEx consists of three interconnected files. Cleanex_exp files store expression data with sample information; CleanEx_targ entries provide the connection between gene names and expression data, and the target annotations are being frequently updated so that they reflect the newest information about genes. The Cleanex file is a catalogues of official gene names, linked to expression datasets, target information, and external databases. The contents of the Cleanex_trg and Cleanex files can be downloaded from an ftp site. All three files can be queried via the web interface.

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Copyright 2009, OpenHelix, LLC.

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