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Similarly, the target genes of compound O were depleted for binding sites of the growth-promoting E2F family of transcription factors.
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Thus these genes can indicate the key biological processes of drug efficacy and represent the sensitivity genes of a compound which can serve as an effective tool for probing the compounds mechanism of action.
For solving these issues additional methodology will be needed for the characterization of esr genes as target genes of estrogenic compounds.
Using this method and four well-characterized reagents, we successfully identified previously known target genes of the compounds as well as other genes involved with functionally related cellular pathways.
Using this algorithm to examine 4718 nonessential gene deletion mutants, the previous known target genes of the compounds and the functionally related genes to these targets were successfully identified and potentially affected cellular pathways were revealed, demonstrating the validity of this approach.
Among them, one Gram-negative strain (ASU-06) was selected and biodegradation ability and initial catabolic genes of petroleum compounds were investigated.
For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways.
Sparse linear programming (SPLP) [ 10] represents a third approach which has been applied to a large microarray dataset derived analyzing from liver gene expression of compound-treated rats.
Besides the biosynthesis genes related to the known compounds, the biosynthetic genes of non-reported compounds in I. indigotica were also indicated by transcriptome annotation.
Comparing the gene expression signature of Compound C (also known as Dorsomorphin), a drug known to inhibit AMPK14, with fractions isolated from the natural product library, FUSION identified several fractions whose biologic activity was similar to Compound C treatment7,28.
Further, PPARγ transactivation and gene expression studies of compound 6c were carried out to investigate the possible mechanism of action through PPARγ modulation.
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