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.