CleanEx database of gene expression profiles

CleanEx provides standardized access to public gene expression data through a dual annotation system to enable integration and comparison of heterogeneous expression datasets.

Key Features:

• Sequence Annotation: Links official gene symbols to measurement sequences including cDNA, Affymetrix arrays, oligonucleotide arrays, SAGE tags, MPSS tags, Expressed Sequence Tags (ESTs), and other mRNA sequences.
• Biomedical Annotation: Annotates experiments with MeSH (Medical Subject Headings) terms standardized by the National Library of Medicine for MEDLINE/PubMed indexing.
• Data Retrieval and Export: Retrieval by gene names or biomedical characteristics and export of numerical expression data as tab-delimited matrix text files supporting single-dataset analysis and cross-dataset comparisons.

Scientific Applications:

• Cross-Dataset Comparisons: Enables joint analyses of gene expression data from different technologies to support comparative and integrative studies.
• Biomedical Research: Facilitates selection and analysis of expression datasets based on biomedical contexts using MeSH annotations to support hypothesis generation and validation.

Methodology:

Sequence annotation links platform-specific measurement sequences to official gene symbols; biomedical annotation assigns MeSH terms to experiments for standardized indexing.