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Components of a Cell (Eukaryotes) Picture from on-line biology book,on-line biology book,

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Presentation on theme: "Components of a Cell (Eukaryotes) Picture from on-line biology book,on-line biology book,"— Presentation transcript:

1 Components of a Cell (Eukaryotes) Picture from on-line biology book,on-line biology book, ~70% water 4% small molecules 15-20% proteins 2-7% DNA/RNA 4-7% membrane

2 Biological databases Data explosion - 96 new 83 updates of well established databases in 201196 new 83 updates - exponential growth of the quantity, complexity and diversity of biological data Protein Data Bank ( - An example of a neuron databaseAn example of a neuron database How to minimize the representation? Earlier individual research oriented databases vs. large scale industrial like databases

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

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

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

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

8 Helix Tracer Helix, density map Helix, true structure 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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