Integrative pathway analysis through

machine learning algorithms

By
Hira azhar (bi113011)
Mariam hanif (bi113002)

Supervisor:
Muhammad Haroon Khan
Co-Supervisor:
Dr Aamer Nadeem

introduction
Cancer is a medical term used for diseases in
which abnormal cells divided.
Cancer cells can spread from one part to
another of the body through the blood

purpose
To understand the algorithm for multiple
networks to find the biological pathways that
accurately classifies the patient disease stage.
Obtain biologically meaningful interpretations
by the results of pathway analysis.
By integrative pathway analysis we will predict
stage and determine the biological
mechanisms.

Problem statment
Pathway analysis on the basis of a single gene
or on the basis of single data type to infer
pathway activities has been proved to be
unable to explore the whole system more
realistically.

Proposed solution
we will use more than one genomic data type
per patient
It will be the realistic model that enhance the
accuracy of integrative models predictions

scope
The scope of the model simulated is not
limited to any organization. It can be used
freely by anyone. This domain is for
researchers, physicians, diagnostic labs as well
as bio technicians. It is a very useful tool that
gives understanding about the integrative
pathway analysis by using machine learning
algorithm.

motivation
The pathway analysis integrating genomic
data types has previously been performed by
testing one gene from the entire pathway. It
was based on single data types. But now we
want to make a tool in which we use more
than one genomic data type (gene expression,
SNPs, DNA methylation) per patient. And use
the entire pathway instead of single gene in
the dataset.

Tools and Technologies
Web-based system
PHP: Hypertext Preprocessor/Java
My SQL database system
Methodology:

deadline

goal

9/24/2014 Project Presentation

( Mid-Term )

Literature search and Algorithms
understanding

Final Project Presentation Part-1

Prototype

Final Project Part-2
(Mid-Term)

Implementation

Final Project

Complete implementation of project and
Testing.

References
The Cancer Genomics Atlas 2013; [cancergenome.nih.gov].
Bell D, Berchuck A, Birrer M, et al. Integrated genomic
analyses of ovarian carcinoma. Nature. 2011;490:60915.
Cancer Genome Atlas Network. Comprehensive molecular
characterization of human colon and rectal cancer. Nature.
2012;487:3307.
Pang H, Datta D, Zhao H. Pathway analysis using random
forests with bivariate
node-split for survival outcomes. Bioinformatics.
2010;26:2508.
Tsuda K, Shin H, Scholkopf B. Fast protein classification
with multiple networks. Bioinformatics. 2005;21:ii59ii65

Thank u