Visualizing differentially expressed genes

Atiq U. Islam; Khan M. Iftekharuddin; David J. Russomanno

doi:10.1117/12.681433

8 September 2006 Visualizing differentially expressed genes

Atiq U. Islam, Khan M. Iftekharuddin, David J. Russomanno

Proceedings Volume 6310, Photonic Devices and Algorithms for Computing VIII; 63100O (2006) https://doi.org/10.1117/12.681433
Event: SPIE Optics + Photonics, 2006, San Diego, California, United States

Abstract

Identification of significantly differentially expressed genes (marker genes) among sample groups is a central issue in microarray analysis. This identification is important to understand the molecular pathway of diseases. Many statistical methods have been proposed to locate marker genes. These methods depend on a cutoff value for selection. A tightfisted cutoff may omit some of the important marker genes, whereas a generous threshold increases the number of false positives. Although robust models for identifying marker genes more accurately is an area of intense research, effective tools for the evaluation of results is often ignored in the literature. Despite the robustness of many of these methods, there is always some probability of false positives. In this paper, we propose a novel approach that exploits parallel coordinates to visualize the gene expression patterns so that one can compare the expression level changes of the marker genes between sample groups and determine whether the selected marker genes are valid. Such visualization is useful to measure the validity of the marker gene selection process as well as to fine tune the parameters of a particular method. A prediction method based on the selected marker genes is used to measure the reliability of our process.

Citation Download Citation

Atiq U. Islam, Khan M. Iftekharuddin, and David J. Russomanno "Visualizing differentially expressed genes", Proc. SPIE 6310, Photonic Devices and Algorithms for Computing VIII, 63100O (8 September 2006); https://doi.org/10.1117/12.681433

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available

Members: $17.00

Non-members: $21.00 ADD TO CART

PROCEEDINGS
12 PAGES

DOWNLOAD PAPER SAVE TO MY LIBRARY

GET CITATION

RIGHTS & PERMISSIONS

Get copyright permission Get copyright permission on Copyright Marketplace

KEYWORDS

Tissues

Visualization

Statistical analysis

Data modeling

Prototyping

Statistical methods

Tumors

Show All Keywords

Keywords/Phrases

Search In:

Publication Years