proint finder to search protein interactions shwe s. lin mentor: matteo pellegrini, ucla
Post on 19-Dec-2015
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ProInt Finder to Search Protein Interactions
Shwe S. LinMentor: Matteo Pellegrini, UCLA
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Outlines
Project overviewPurposeBackgroundMy partAlgorithmsTool usedExamplesAcknowledgmentsReferences
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Project Overview
To develop a protein-protein interaction database and an interactive web-based interface to search for protein interactions from the database
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Purpose of the Project
To study protein-protein interactions• Example: p53-MDM2 interactions
To predict protein functions which may be inferred from analyzing protein interactions • Example: protein A interacts with 5 cell cycle proteins
and we therefore infer that it is a cell cycle protein
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Importance of Studying Protein Interactions
Example:
Essential for cell communications which result in activation or inactivation of biological responses
• Protein MDM2 inactivates p53’s function as a
tumor suppressor
• EPO interacts with the EPO receptor to trigger growth of erythrocytes
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Traditional Methods for Studying Protein Functions
• Sequence alignment techniques
• Protein’s 3-D structure
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Limitations of Traditional Methods
Yield functional information only on experimentally characterized homologous proteins
Detect protein’s biochemical function only;
not biological process
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Approach to Address Limitations
Develop protein interaction databases • Example: DIP, MINT, BIND etc.
Implement methods for function prediction • Example: guilt-by-association
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My Part
Develop web application (ProInt Finder) to utilize the database for studying protein interactions
• Django: Python Web framework
• Database: Automated collections of data by text mining of web
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Algorithm (Input)
Accept query: gene name or gene id of interest • Example - Gene name: p53
Gene ID: 7157
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Algorithm (Search)QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture. Search for gene_ids from the database gene
table
actors acted by
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Algorithm (Output)
Return: gene_1_id interacts with gene_2_id Result: List of protein pairs that are experimentally identified to interact with each other
pro_ A >> activates pro_B pro_E phosphorylates >> pro_A
>> acetylates pro_C pro_H binds to >> >> methylates pro_D pro_I activates >> >> interacts with pro_E pro_K regulates >>
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Tool Used: Django
• Python web framework to build Web applications• Provides Model-View-Controller (MVC)
approach to programming• Database layer: Models or data models• Controller layer: View or control logic• View layer: Templates or user interface
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• Each model is a Python class • Contains fields and behaviors of the stored data• Each model maps to a single database table
Database Layer: Models
Gene
A Model in Django
Gene ID
Gene Name
Taxonomy ID
from django.db import modelsclass Gene(models.Model): gene_id = models.IntegerField (primary_key=True) long_name = models.TextField( ) symbol = models.TextField( ) tax_id = models.ForeignKey( Species )
class Meta: db_table = 'protInt_gene' ordering = ['symbol']
Fields/ class attributes
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View Layer: Templates
ProInt Finder• A text file that contains variables and tags
• Variables: Get replaced with values when the template is evaluated • Tags: Control the logic of the template
Templates for each of the web pages for ProInt Finder
index.html results.htmlsearch.html
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Control Layer• Takes user input from search.html template
• Defines how to process the data
• Returns results to results.html template
search.html
User input
Controller(View)
results.html
Protein interactions
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Home Page
This is a link which leads to the search page.
These are links to other protein interaction databases.
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Search page
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Result page
User Input
Description of the protein
Query protein interacts with different protein
Proteins interacts with query protein
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More on Result
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Web Links
Click on the link
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Acknowledgements
Dr. Matteo Pellegrini Shawn Cokus Joseph Kim and Cory Tobin Dr. Sandra Sharp and Dr. Wendie
Johnston SoCalBSI NIH, NSF, and LAOC
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References
• http://www.djangoproject.com/
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Questions?