Spot Characterization in Proteomics and Jet Analysis in Heavy Ion Collision

B.Tech. Project Stage 1 Presentation

Nikhil Prakash 09026015

Department Of Physics,IIT Bombay November 28,2012

Outline
Proteomics Introduction Heavy Ion Collisions Wavelet Neural Networks Mathematical Morphology Conclusions

Proteomics
Protein + Genome = Proteome Total Number of Proteins in a Cell at a given Time are called Proteome. Analysis of this Proteome Proteomics. Analysis includes Identification and Sequencing of Proteins.

Two Dimensional Electrophoresis Gel Image

Used as Separation Tool of Proteins in Proteomics. Separation Parameters Used
Molecular Mass Isoelectric Point

Contains 2000+ Protein Spots Digital Analysis of these gels are used for Identification of the Protein Spots

Principle of Two-Dimensional Gel Electrophoresis : A Extraction Of Proteins B1 Sample Loaded on pH Gradient B2 Sample is Neutralized C Strip is then Equilibrated in a SDS(sodium dodecyl sulfate) D This is then loaded on top of a SDS PAGE (Polyacrylamide Gel Electrophoresis) gel and Proteins gets separated on the basis of their molecular masses. Image from [1]

A Typical Two Dimensional Electrophoresis Image (2DGE) with red circles showing few Protein Spots Image Courtesy: http://www.pierroton.inra.fr/genetics/2D/

A Typical Protein Spot in 2DGE Image

Challenges in 2DGE Image Analysis

Background contains Horizontal and Vertical Streaks and is highly varying. Faint and Weak Protein Spots Overlapping Spots

Heavy Ion Collisions

It is proposed that a Hot, Dense medium Quark Gluon Plasma is Formed in Relativistic Heavy Ion Collisions.[8] QGP Consists of Elementary Particles. QGP Transitions are probed to Understand the Dynamics of the Universe.

http://en.wikipedia.org/wiki/File:Standard_Model_of_Elementary_Particles.svg

Jet Analysis
In QGP, Particle like Hadrons cannot exist in Free Form. Become Clusters of Particles known as Jets Energy and Momentum of these Jets are Correlated. Clustering Algorithms are Used to Study these Jets. Analyzing these Clusters are sub-images in the whole Detected Image

Jets Detected by ALICE(A Large Ion Collider Experiment) Image from : http://news.discovery.com/space/in-the-beginning-the-universe-was-a-liquid.html

Wavelet Neural Networks

Feed-Forward (1+1/2) Architecture Network. Hidden Layer Activation Functions derived from Orthonormal Wavelet Family. Proved to be Best Estimators for Learning Dynamic Systems[14][15]

A Typical Wavelet Neural Network

WNN Learning
Wavelet Network is Defined as

Parameters are Learned by following Equations:

Mathematical Morphology
Set Method of Image Analysis to get Quantitative Description of Geometrical Structures developed by Serra[20] and Matheron[21] Tool for Extracting Useful Knowledge from the Image. Generally, Used for Binary Images but recently Extended for Gray-Scale Images

Structuring Element (SE)

Basic sub-image used in Mathematical Morphology to Probe the Image.

Structuring Elements with circled pixels as Origin

Basic Operations in MM
Operations are based on Expanding and Shrinking the Images. Basic Operation
Dilation Erosion

Dilation
Dilation can be viewed as a set of locus of the all points covered by center of the structuring element B in the image set A. Mathematically, Dilation is defined as

Image A is dilated by Structuring Element B Image from [22]

Erosion
Erosion can be viewed as a set of locus of the points of the origin of structuring element covered by the B inside the image set A. Mathematically, Erosion is defined as

Image A is eroded by Structuring Element B Image from [22]

Hit and Miss Transformation

Hit and Miss Transformation(HMT) extracts the information of a particular shape in the Image. Uses Two SEs
For Matching Foreground of the Shape For Matching Background of the Shape

Mathematically, HMT is defined as

or

Position of Subset D is Extracted in Image using Hit and Miss Transformation [22]

Pattern Matching using HMT and WNN

Modeling the Structuring Elements using WNNs for detecting the sub-images Using these SEs, detecting the patterns in the Image. A Similar Technique is used for Detecting Stars from the Astronomical Data

Structuring Elements used in detection of Stars in Low Brightness Galaxies Image Courtesy: http://www.sciencedirect.com/science/article/pii/S003132030900082X

Conclusions
From the Success of detection of Stars from Astronomical data, We can say that the technique will work in Proteomics as Spots in 2DGE Image and Stars in Galaxies have similar difficulties in Analysis.

Thank You

References
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