Browsing by Subject "multivariate analysis"
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Item Open Access Development of a WEB application(Bilkent University, 2011) Kaya, Koray DoğanmicroRNAs, small non-coding RNA molecules with important roles in cellular machinery, target mRNAs for silencing by binding generally to their 3’ UTR sequences via partial base complementation. Thus, microRNAs with similar sequences also might exhibit expression and/or functional similarities. In this study, a modular tool, mESAdb (http://konulab.fen.bilkent.edu.tr/mirna/), was developed allowing for multivariate analysis of sequences and expression of microRNAs from multiple taxa. Its framework comprises PHP, JavaScript, packages in the R language, and a database storing mature microRNA sequences along with microRNA targets and selected expression data sets for human, mouse and zebrafish. mESAdb allows for: (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by a sequence motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HuGE Navigator, KEGG and GO. mESAdb also permits user specified dataset upload for these analyses. Herein, utility of mESAdb was illustrated using different datasets and case studies. First, it was shown that microRNAs carrying the embryonic stem cell specific seed sequence, ‘AAGTGC’, were able to discriminate between normal and tumor tissues from hepatocellular carcinoma patients using dataset GSE10694. Second, mRNA targets of a set of liver specific microRNAs were annotated with human diseases based on HuGE Navigator. Third, the similarity between mouse and human tissue specificity of a given set of microRNAs was demonstrated. Forth, CHRNA5 targeting microRNAs were associated with estrogen receptor status in breast cancer using dataset GSE15885. Finally, a related tool under development for mRNA arrays planned for integration with mESAdb was presented.Item Open Access Using neutron activation analysis to identify scales of interaction at Kinet Höyük, Turkey(2008) Grave P.; Kealhofer L.; Marsh, B.; Gates, M.-H.We use NAA to characterize a relatively large archaeological ceramic sample from the Late Bronze Age to Hellenistic phases of Kinet Höyük, a coastal Turkish site in the Gulf of Iskenderun at the northeast corner of the Mediterranean Sea. The geographic extent of local Kinet wares (how local is local?) is established through comparison with sediment samples across the Kinet hinterland. Four major compositional groups are identified: local and locally imported wares, imports from Cypriot, and presumed Western Anatolian and Aegean centers, and imports that appear relatively homogenous elementally but comprise typologically diverse ceramics with attributions that range from Cyprus to the coastal mainland. Comparison with other published NAA studies for this site reinforces the elemental evidence for local production, and underlines the need for caution when assuming local production always equates with local clays particularly for coastal sites. We propose that the chronological distribution of the local and non-local groups provides a useful political economic proxy. The study indicates systemic and widespread political disruption and marginalization at the transition to the Late Iron Age in this region. © 2008 Elsevier Ltd. All rights reserved.