The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury

Journal of Research in Medical Sciences : the Official Journal of Isfahan University of Medical Sciences
Kobra Moradzadeh, Yousof Gheisari

Abstract

Acute kidney injury is a common debilitating disease with no curative treatment. The recent development of big biological data is expected to expand our understanding of the disorder if appropriately analyzed to generate translational knowledge. We have here re-analyzed a time-course microarray data on mRNA expression of rat kidneys exposed to ischemia-reperfusion to identify key underlying biological processes. The dataset was quality controlled by principal component analysis and hierarchical clustering. Using limma R package, differentially expressed (DE) genes were detected which were then clustered according to their expression trajectories. The biological processes related to each cluster were harvested using gene ontology enrichment analysis. In addition, the interaction map of proteins encoded by the DE genes was constructed, and the functions related to network central genes were determined. Furthermore, signaling pathways related to the DE genes were harvested using pathway enrichment analysis. We found 8139 DE genes that drive critical processes such as the control of blood circulation, reactive species metabolism, mitochondrial respiration, apoptosis, cell proliferation, as well as inflammatory and immunological rea...Continue Reading

References

Apr 4, 2018·Genomics·Kobra MoradzadehYousof Gheisari

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Datasets Mentioned

BETA
GSE58438

Software Mentioned

REViGO
limma
Eulerr
pheatmap
Short Time - Series Expression Miner
R
ClueGO
Sketch
Bioconductor
ggplot2

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