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As transcription factors normally influence gene expression of several downstream targets and, thus, are likely to play a fundamental role in this concept, we used gene expression patterns of transcription factors to illustrate the LARGE concept.
We used gene expression patterns attributable to chemotherapy-resistant cells to detect potential new biomarkers related to anthracycline resistance.
In our earlier study, we used gene expression patterns of closely related chemotherapy-resistant and -sensitive parental cancer cell lines to identify discriminatory genes associated with drug resistance.
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In this study, we use gene expression patterns to explore the activation of various epigenetic pathways across human cancers.
We therefore utilised this system to analyse the molecular dynamics of tumours arising in mice following asbestos exposure, using gene expression patterns as a readout.
A promising genomic approach to this problem uses gene expression patterns measured across the genome for dozens of cell lines compared to patterns of chemosensitivity drug panels measured across the same cell lines.
Just as it is important to select tag SNPs based on allele correlations in a population similar to the population studied, it is also important to use gene expression patterns from the specific tissue of interest [ 18].
This model enables analysis of the molecular events associated with asbestos induced mesothelioma and is utilised here to investigate the molecular dynamics of tumours induced in these mice, using gene expression patterns as a read out.
Informatics-based approaches to drug repositioning are exemplified by the identification of known drug targets in genes arising in genome-wide association studies [ 8], the prediction of structural suitability of a known compound for a new protein target [ 9, 10], systems biology using gene expression patterns [ 6, 11], and the study of side effects [ 12].
The fate of the B. rapa homologues was determined using gene expression pattern and sequence diversification rates compared to pivotal genes.
They demonstrated that different mutants or chemical treatments affecting similar cellular processes induce similar expression profiles, suggesting that the compendium could be used to characterise the mechanism of pharmacological perturbations by using gene expression pattern-recognition algorithms.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com