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Related Experiment Video

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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published on: May 9, 2017

CrossQuery: a web tool for easy associative querying of transcriptome data.

Toni U Wagner¹, Andreas Fischer, Eva C Thoma

¹Physiological Chemistry I, Biocenter, University of Würzburg, Würzburg, Germany. toni.wagner@biozentrum.uni-wuerzburg.de

|December 17, 2011

Summary

CrossQuery is a web tool simplifying transcriptome sequencing and microarray data analysis for researchers. It allows easy filtering, sorting, and correlation of complex biological datasets with minimal computational expertise.

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Modern sequencing technologies generate vast biological datasets.
Complex primary analyses require specialist expertise.
Biomedical researchers need accessible tools for secondary data analysis.

Purpose of the Study:

To introduce CrossQuery, a web tool for non-specialists.
To enable straightforward querying of transcriptome sequencing and microarray data.
To facilitate data filtering, sorting, and cross-association.

Main Methods:

Development of a web-based tool, CrossQuery.
Utilized deep-sequencing data from Medaka fish stem cells.
Employed microarray data from human endothelial cells.
Implemented simple syntax for data queries.

Main Results:

CrossQuery allows correlation, filtering, and sorting of mRNA expression, gene/transcript IDs, GO-terms, and gene descriptions.
Queries can be saved and results exported to standard formats compatible with tools like Microsoft Excel.
The tool supports the association of multiple datasets sharing common identifiers (e.g., transcript IDs, GO-terms).

Conclusions:

CrossQuery empowers researchers to work with complex omics data efficiently.
Minimal computer skills are required for effective data exploration.
The tool's design supports extensibility for advanced users and new data types.