Search results for "microarray."
showing 10 items of 384 documents
Infrequent promoter methylation of the MGMT gene in liver metastases from uveal melanoma.
2008
Uveal melanoma is associated with a high mortality rate once metastases occur, with over >90% of metastatic patients dying within less than 1 year from metastases to the liver. The intraarterial hepatic (iah) administration of the alkylating agent fotemustine holds some promise with response rates of 36% and median survival of 15 months. Here, we investigated whether the DNA-repair-protein MGMT may be involved in the variability of response to fotemustine and temozolomide in uveal melanoma. Epigenetic inactivation of MGMT has been demonstrated to be a predictive marker for benefit from alkylating agent therapy in glioblastoma. We found a methylated MGMT promoter in 6% of liver metastases fr…
The role of NFkappaB inducing kinase (NIK) in the pathogenicity of EAE
2014
pathways (PTPN6, SLC3A2, VAV3, DDR1) and modulators of oxidative stress (MT1A, HMOX1, SLC30A1) were also significantly affected by the CBD treatment. The microarray results were confirmed using qPCR on selected gene targets. Immunoblotting demonstrated that CBD reduces IL-17 by decreasing STAT3 phosphorylation and increasing that of STAT5. In conclusion, our observations increase our understanding of the mechanisms of the anti-inflammatory activities of CBD.
Convolutional architectures for virtual screening
2020
Abstract Background A Virtual Screening algorithm has to adapt to the different stages of this process. Early screening needs to ensure that all bioactive compounds are ranked in the first positions despite of the number of false positives, while a second screening round is aimed at increasing the prediction accuracy. Results A novel CNN architecture is presented to this aim, which predicts bioactivity of candidate compounds on CDK1 using a combination of molecular fingerprints as their vector representation, and has been trained suitably to achieve good results as regards both enrichment factor and accuracy in different screening modes (98.55% accuracy in active-only selection, and 98.88% …
iGEMS : an integrated model for identification of alternative exon usage events
2016
DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug,…
Effects of postharvest partial dehydration and prolonged treatments with ethylene on transcript profiling in skins of wine grape berries.
2010
For certain food products, postharvest controlled stresses or treatments with specific elicitors are applied to induce desired physical/chemical changes and/or to positively affect phytochemical content. This is the case of wine grapes where both strategies, singularly applied or coupled, can be used to modulate berry composition and, as a consequence, affect wine quality traits. Since the knowledge of the effects of these postharvest treatments on berry metabolism and the regulation of gene expression is very limited, a large-scale transcriptome analysis has been carried out, using an oligo-based microarray (14,562 probes) on skins of wine grape (Vitis vinifera L.) berries subjected to deh…