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      • Theses - Department of Molecular Biology and Genetics
      • Dept. of Molecular Biology and Genetics - Master's degree
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      •   BUIR Home
      • University Library
      • Bilkent Theses
      • Theses - Department of Molecular Biology and Genetics
      • Dept. of Molecular Biology and Genetics - Master's degree
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      Analyses and web interfaces for protein subcellular localization and gene expression data

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      Author
      Bilen, Biter
      Advisor
      Çetin-Atalay, Rengül
      Date
      2007
      Publisher
      Bilkent University
      Language
      English
      Type
      Thesis
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      Abstract
      In order to benefit maximally from large scale molecular biology data generated by recent developments, it is important to proceed in an organized manner by developing databases, interfaces, data visualization and data interpretation tools. Protein subcellular localization and microarray gene expression are two of such fields that require immense computational effort before being used as a roadmap for the experimental biologist. Protein subcellular localization is important for elucidating protein function. We developed an automatically updated searchable and downloadable system called model organisms proteome subcellular localization database (MEP2SL) that hosts predicted localizations and known experimental localizations for nine eukaryotes. MEP2SL localizations highly correlated with high throughput localization experiments in yeast and were shown to have superior accuracies when compared with four other localization prediction tools based on two different datasets. Hence, MEP2SL system may serve as a reference source for protein subcellular localization information with its interface that provides various search and download options together with links and utilities for further annotations. Microarray gene expression technology enables monitoring of whole genome simultaneously. We developed an online installable searchable open source system called differentially expressed genes (DEG) that includes analysis and retrieval interfaces for Affymetrix HG-U133 Plus 2.0 arrays. DEG provides permanent data storage capabilities with its integration into a database and being an installable online tool and is valuable for groups who are not willing to submit their data on public servers.
      Keywords
      protein subcellular localization prediction
      proteome
      web interface and database
      eukaryotic model organisms
      microarray gene expression
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      http://hdl.handle.net/11693/29941
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      • Dept. of Molecular Biology and Genetics - Master's degree 135
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