CleanEx Tutorial

CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.

Direct AccessExpression Data Related ToolsAnalysis ToolsData Extraction ToolsMeSH oriented toolsDocumentationLinks
Current release is based on Unigene database available on : 11 Jun 2008

Direct Access to CleanEx Individual Entries

in CleanEx database by ID or GENE SYMBOL


in CleanEx Target database by Target ID(see here for format help)

CleanEx Individual Entries with Selected Expression Datasets
Extract gene and selected expression data Allows to extract CleanEx individual entries together with datasets selected according to their biological/medical annotation from the MeSH terms tree. Only datasets corresponding to all the terms checked will be selected
Extract gene and selected expression data (advanced users) Same as above, but for the dataset's specifications part, you can directly enter a list of MeSH terms instead of walking down the MeSH tree. You also have the possibility to join the dataset's associated MeSH terms with other operators than the AND operator. This tool works also with "free text search", but remember that free text IS NOT controlled vocabullary
Expression Dataset's Related General Tools
Dataset List Shows the complete list of expression datasets included in CleanEx. Datasets are classified according to the organism and to the data generation system (Affymetrix, Dual Channel, Basic Ratio or Counts experiments)
Finding expression datasets in CleanEx Text search in the datasets description lines. The list of terms to search can be either "free text" ot "MeSH terms" based. The MeSH term search is more precise
Finding individual experiments from different expression datasets in CleanEx Text search in the datasets and experiments description lines. The list of terms to search can be either "free text" ot "MeSH terms" based. The MeSH term search is more precise
Common Genes List across datasets From a given dataset list, extracts all the features representing common genes between these datasets. The ouput lists the HUGO Gene Symbols as well as the individual "Spots" or "Probesets" in each dataset

General Data Extraction Tools
Extract expression data Extract numerical data as well as experiment and "feature" descriptions from an expression dataset included in CleanEx. Output is a data matrix with the two description files. Extraction field can be chosen by the user
FTP Site Download all CleanEx files via the FTP repository

MeSH oriented Data Extraction Tools
Extract expression data Extract numerical data as well as experiment and "feature" descriptions from an expression dataset included in CleanEx. Output is a data matrix with the two description files. Extraction field can be chosen by the user. The dataset is selected via a tree-based biological conditions selection. Data extraction then proceeds as above (Extract expression data)
Cross-dataset data extraction Same as above, but allows data extraction coming from different datasets. Numerical values are "re-scaled" for each experiment (sample) and go from 1 to 1000. For dual channel, only the "red" channel is taken into account

Analysis Tools
Step-by-step Going from one dataset, extract specific gene list (over-represented on under-represented). From the generated list, and through another dataset, extracts trends which are common to both datasets
Experiments pools comparison From the MeSH terms list, generate two data pools according to user-selected biological criteria, then extracts the corresponding common genes and numerical data, and processes to a differential analysis between the two pools
Experiments pools comparison
Advanced users
Same as above, but you can directly enter a list of MeSH terms instead of walking down the MeSH tree. This tool works also with "free text search",, but remember that free text IS NOT controlled vocabullary
Batch From an input list containing either gene names or sequence references, clone names, SAGE or MPSS tags or Affymetrix probesets, gives for each input feature the corresponding gene symbol, sequence reference, or Unigene cluster

General Documents
CleanEx user manual
Survey of most recent release
List of examples from CleanEx and CleanEx Target
CleanEx Reference paper : "CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature.". Praz V, Jagannathan V, Bucher P. Nucleic Acids Res. 2004 Jan 1;32:D542-7. PMID: 14681477.

Access to servers offering related services
SOURCE Genomic resource of functional annotations, ontologies, and gene expression data
GEOGene Expression Omnibus, a resource for gene expression data repository, browsing, query and retrieval
SMDThe Stanford Microarray Database
ArrayExpressPublic repository for microarray data annotated in accordance with MGED recommendations

Access to other databases and tools on the SIB-Lausanne server
EPDThe eukaryotic Promoter Database
SSAThe Signal Search Analysis Server
myHITSA database and web tools devoted to protein domains
EMBnetSwiss Node Of The EMBnet Group
Last update March 2014