Prediction and Analysis of Retinoblastoma Related Genes through Gene Ontology and KEGG

Min Jiang,Biqing Li ,Tao Huang,Lei Chen,Lin Liu,Jian Zhang,Zhen Li

doi:10.1155/2013/304029

Abstract

One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well.

Highlights

Retinoblastoma (Rb) is a rapidly developing cancer in infants that develops in the cells of retina, the light-detecting tissue of the eye [1], which can be heritable or nonheritable
1061 Gene Ontology (GO) terms and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were obtained as the optimal features to discriminate an RB and non-RB gene, which has been shown to be closely related to RB
After running the maximum relevance minimum redundancy (mRMR) software, we obtained two tables for each of the ten datasets: one is called MaxRel feature table that ranks the features according to their relevance to the class of samples and the other is called mRMR feature table that lists the ranked features by the maximum relevance and minimum redundancy to the class of samples

Summary

Introduction

Retinoblastoma (Rb) is a rapidly developing cancer in infants that develops in the cells of retina, the light-detecting tissue of the eye [1], which can be heritable or nonheritable. The most common and obvious sign of retinoblastoma is an abnormal appearance of the pupil, leukocoria, known as amaurotic cat’s eye reflex [2]. Retinoblastoma is rare and affects approximately 1 in 15,000 live births, but it is the most common inherited childhood malignancy. In China, around 1100 new cases are diagnosed each year, just second to that of India. In about two-thirds of cases, only one eye is affected (unilateral retinoblastoma); in the other third, tumours develop in both eyes (bilateral retinoblastoma). The number and size of tumours on each eye may vary [2]

Methods

Results

Conclusion