Components of a Cell (Eukaryotes)
-
Upload
noelle-figueroa -
Category
Documents
-
view
44 -
download
2
description
Transcript of Components of a Cell (Eukaryotes)
Components of a Cell (Eukaryotes)
Picture from on-line biology book, http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html
~70% water4% small molecules15-20% proteins2-7% DNA/RNA4-7% membrane
Biological databases
• Data explosion - 96 new 83 updates of well established databases in 2011 - exponential growth of the quantity, complexity and diversity of biological dataProtein Data Bank (www.pdb.org) - An example of a neuron database How to minimize the representation?
• Earlier individual research oriented databases vs. large scale industrial like databases
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
Computations in Proteomics
• Introduction to MS
• 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
Computations in Proteomics
Enright et al., Nature 402 p86-90
• Protein-protein interactions- Use genomic sequencesfusion event detection through computation
• Modeling gene regulatory network- nodes: genes/proteins- edges: biological events- inputs: proteins (eg. transcription factors)- outputs: gene expression
Microarry Data• Microarray technology• Microarray gene expression databases
(eg. GEO GSE17913), interested in co-expression of genes, relationship of genes,system biology, pathways
• PubMed literature databasesExtract the knowledge from literatures, text mining
Literature Data
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
Helix Tracer
Helix, density map Helix, true structure
Protein 1BM1Del 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.