| Type: co-expressed gene pair |
GRN ID: re123172 |
Name: |
Validated: N |
| Direction: |
Unknown or N/A |
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| References: |
- Li J, Wei H, Liu T, Zhao PX. GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data. Nucleic Acids Res. 2014 Mar;42(5):e32. doi: 10.1093/nar/gkt983. Epub 2013 Oct 30. PubMed PMID: 24178033; PubMed Central PMCID: PMC3950724.
- Transcriptomic data is potential to associate co-expressed genes through expression pattern analysis. Total 29 microarray experiments, including around 300 hybrid assays, were manually collected from ArrayExpress database; all of them are based on Affymetrix 22k chip and designed to include control and hormone treatment over multiple tissues and organs. The raw data were normalized with R language ‘affy’ module.
We further analyze the normalized expression data using our superfast high-performance gene network prediction server, GPLEXUS (http://plantgrn.noble.org/GPLEXUS/). The threshold of Spearman-based mutual information value between genes, i.e., gene association value, was set to 0.5 to only keep the edges that reflect the gene pair with similar expression pattern. Here the gene association value represents the similarity of expression pattern between genes across the Microarray experiments. The higher the value is; the more similar the expression pattern of gene pair is. Similar expression pattern may implicit the potential relationship between genes.
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