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Evaluating the Interactions of Silver Nanoparticles and Mammalian Cells Based on Biomics Technologies
Published in Huiliang Cao, Silver Nanoparticles for Antibacterial Devices, 2017
GenMAPP was utilised for biological pathway analysis for 257 matched miRNA target mRNAs and target proteins, and 57 pathways were found to have participated. The number of involved pathways rose from 18 (Ag NP 1 h) to 45 (Ag NP 4 h and Ag NP 8 h), which suggested that the effect of miRNAs on target mRNAs/proteins increased with the passage of time.
Survival genes expression analysis following ionizing radiation to LiCl treated KG1a cells
Published in International Journal of Radiation Biology, 2020
Yogesh Kumar Verma, Ajay Kumar Singh, Gangenahalli Ugraiah Gurudutta
Transcript probes which were reliably detected in all the replicates (n = 3) were considered for subsequent data analysis. The data were normalized by the percentile shift normalization method using GeneSpring GX12.1 (Agilent technologies). Following normalization, the data were log2 transformed. Differentially regulated genes were identified based on average log2 ratio and p ≤ .05. The MIAME compliant intensity, quality and normalized ratio data were deposited in the Gene Expression Omnibus database (GSE102129). To identify biological processes and molecular functions represented by the differentially regulated genes, functional annotation tool of the DAVID Bioinformatics Resources 6.7 was used (Huang et al. 2009). Further, the signaling pathways regulated by significantly altered genes were identified, which provided annotation from KEGG, Biocarta and GenMAPP, taking Fisher exact p ≤ .05 as significant.
α-Casein Changes Gene Expression Profiles and Promotes Tumorigenesis of Prostate Cancer Cells
Published in Nutrition and Cancer, 2020
Joo-Young Kim, Seong Ik Bang, Sang Don Lee
Hybridized images were scanned using Agilent’s DNA microarray scanner and quantified using Feature Extraction Software (Agilent Technology). All data normalization and selection of fold-change changes in gene expression were performed using GeneSpringGX 7.3 (Agilent Technology). The averages of normalized ratios were calculated by dividing the average of the normalized signal channel intensity by the average of the normalized control channel intensity. Functional annotation of genes was performed according to the Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) using GeneSpringGX 7.3. Gene classification was based on searches performed of the BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/). Kyoto Encyclopedia of Genes and Genomes (KEGG) molecular pathway analysis was performed for identification of possible enrichment of genes with specific biological themes (http://www.genome.jp/kegg/pathway.html).