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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Comparative modular analysis of gene expression in vertebrate organs
Barbara Piasecka1, Zoltán Kutalik, Julien Roux
1Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1005 Lausanne, Switzerland.
BMC Genomics
|March 31, 2012
Summary
Gene expression conservation across homologous organs is revealed by a novel modularization approach. This method identifies conserved gene modules in mouse, human, and zebrafish, highlighting functional similarities and exceptions like the testis.
Area of Science:
- Comparative genomics
- Systems biology
- Gene expression analysis
Background:
- The conservation of gene expression across homologous organs between species is not well understood.
- Previous studies often analyzed all orthologous genes, including those not specific to organ function.
- A more refined approach is needed to accurately assess cross-species organ expression similarity.
Purpose of the Study:
- To develop and apply a novel method for identifying conserved gene expression patterns between homologous organs across species.
- To investigate the extent of gene expression conservation in mouse and human organs using microarray data.
- To explore functional coherence and evolutionary patterns of gene expression modules.
Main Methods:
- Utilized a modularization algorithm to identify inter-species co-modules of organs and genes.
- Applied the algorithm to mouse and human microarray expression data.
- Validated findings using zebrafish orthologs and functional enrichment analysis.
Main Results:
- Identified functionally coherent gene and organ co-modules conserved across mouse, human, and zebrafish.
- Found a significant proportion of orthologous genes within conserved co-modules.
- Observed exceptions to conservation, notably in the testis and olfactory bulb, and identified functionally related organ groupings.
Conclusions:
- The study introduces a new framework for comparative analysis of large-scale phenotypic data across species.
- The modularization approach effectively reveals conserved gene expression patterns in homologous organs.
- This method provides a robust tool for future cross-species biological data analysis.
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