Browsing by Subject "database"

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    Development of a WEB application
    (2011) Kaya, Koray Doğan
    microRNAs, 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.
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    ItemOpen Access
    Recoding the nautical archaeology : virtual museum of underwater cultural heritage
    (2011) Varinlioğlu, Güzden
    The preservation of underwater cultural heritage requires the availability and access to data produced by nautical archaeology alongside tools for analysis, visualization and communication. Although numerous archaeological surveys and excavations have been carried out in the past decades in Turkey, there is no publicly available information system integrated to nautical archaeology. This dissertation proposes a framework of a virtual museum of underwater cultural heritage (VM). VM incorporates the practices of collection, preservation, research, visualization and exhibit, thus offers new approaches to the preservation of cultural heritage. In this dissertation, a web-based information system has been developed for a model of virtual museum using the data collected during underwater surveys conducted on the coastal region of Kaş, Turkey in 2007-2010. Divers from a variety of professional backgrounds followed the practice of in situ preservation, collecting visual, geographical and descriptive data using structured datasheets. Through the analysis of these nondestructive methods, an information system and a data collection methodology are developed aiming the contribution of all interested parties in a collaborative manner. The system currently contains information on c.600 finds in the form of sketches, measurements, drawings, photographs of finds. Combined with Google Maps, the database illustrates the initial technological steps towards the development of a virtual museum. Divers, archaeologists and other interested users of this information system participate in the musealization of information through separately applied analysis, visualization and communication tools by open software programs. These initial steps demonstrate the methods for the automation of data analysis and visual documentation, the visualization of information and the communication of this knowledge. Futuristic concepts of automated, immersive and interactive design redefine the virtual museum of underwater cultural heritage as well as offer different approaches to the discipline of nautical archaeology.