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Related Experiment Video

Updated: Jan 2, 2026

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

Published on: September 28, 2019

CleanEx: new data extraction and merging tools based on MeSH term annotation.

Viviane Praz¹, Philipp Bucher

¹ISREC, Swiss Institute of Bioinformatics, Boveresses 155, Epalinges, VD 1066, Switzerland. viviane.praz@unil.ch

Nucleic Acids Research

|December 17, 2008

Summary

This summary is machine-generated.

The CleanEx database offers access to gene expression data, linking gene symbols to various sequence types and annotating experiments with Medical Subject Headings (MeSH) terms for easier retrieval of biological and medical information.

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Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Public gene expression data is crucial for biological research.
Efficiently accessing and analyzing this data presents a significant challenge.
Existing databases may lack comprehensive annotation for biomedical characteristics.

Purpose of the Study:

To develop a comprehensive gene expression database, CleanEx.
To facilitate access to public gene expression data through dual annotation.
To enable retrieval of expression data based on gene names and experimental biomedical features.

Main Methods:

Implemented a dual annotation system for sequences and experiments.
Linked official gene symbols to diverse gene expression measurement sequences (e.g., cDNA, Affymetrix, SAGE, ESTs).
Re-annotated experiments using Medical Subject Headings (MeSH) terms for biomedical context.

Main Results:

Created the CleanEx expression database (http://www.cleanex.isb-sib.ch).
Enabled gene expression data retrieval by gene symbols and MeSH terms.
Facilitated export of numerical data in tab-delimited text file format.

Conclusions:

The CleanEx database enhances accessibility to public gene expression data.
Dual annotation improves data retrieval based on biological and medical relevance.
Provides a valuable resource for researchers analyzing gene expression patterns.