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Components of a Cell (Eukaryotes)

Components of a Cell (Eukaryotes). ~70% water 4% small molecules 15-20% proteins 2-7% DNA/RNA 4-7% membrane. Picture from on-line biology book, http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html. Biological databases.

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Components of a Cell (Eukaryotes)

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  1. Components of a Cell (Eukaryotes) ~70% water 4% small molecules 15-20% proteins 2-7% DNA/RNA 4-7% membrane Picture from on-line biology book, http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html

  2. Biological databases • Earlier individual research oriented databases vs. large scale industrial like databases • Data explosion • - 96 new 83 updates of well established databases in 2011 • - exponential growth of the quantity, complexity and diversity of biological data • Protein Data Bank (www.pdb.org) • - An example of a neuron database • How to minimize the representation?

  3. Biological databases • Primary Databases : • - nucleic acid sequences including whole genomes • - amino acid sequences of proteins • - protein and nucleic acid structures • - small molecule crystal structures • - protein functions • - expression of genes • - networks: of metabolic pathways, of gene and protein interactions, of control cascades • - publications • Specialized Databases

  4. Computations in Proteomics • Newer Techniques • Mass spectrometry (MS) • - large scale of study of proteins • - anytime, any cells • Introduction to MS • Determination of the content in a complex of proteins • Determination of protein-protein interactions

  5. Computations in Proteomics • Protein-protein interactions • - Use genomic sequences • fusion event detection through computation Enright et al., Nature 402 p86-90 • Modeling gene regulatory network • - nodes: genes/proteins • - edges: biological events • - inputs: proteins (eg. transcription factors) • - outputs: gene expression

  6. Microarry Data • Microarray technology • Microarray gene expression databases • (eg. GEO GSE17913), interested in co-expression of genes, relationship of genes, • system biology, pathways Literature Data • PubMed literature databases • Extract the knowledge from literatures, text mining

  7. Computations in 3D images • Imaging techniques • - Magnetic Resonance Images (MRI) – good tissue contrast, tumor detection, 2003 Nobel Price (Paul Lauterbur, Sir Peter Mansfield) • - CT • - Electron tomography (eg. portal proteins) • 3D Volumetric data • - pattern recognition, registration, classification, image retrieval, image data mining

  8. Helix Tracer Helix, true structure Helix, density map Protein 1BM1 Del Palu, A., He. J., Pontelli, E., Lu, Y. “Identification of -helices from Low Resolution Protein Density Map” Proceedings of Computational Systems Bioinformatics (CSB) 2006, p89-98, Stanford University, Aug. 2006.

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