GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis

Mathur Sachin,Visvanathan Mahesh,Smith Peter G,Lushington Gerald H,Srinivas Adagarla B,Yoo Byunggil,Svojanovsky Stan

doi:10.2174/1875036200903010026

Abstract

We have developed the web based tool GOAPhAR (Gene Ontology, Annotations and Pathways for Array Research), that integrates information from disparate sources regarding gene annotations, protein annotations, identifiers associated with probe sets, functional pathways, protein interactions, Gene Ontology, publicly available microarray datasets and tools for statistically validating clusters in microarray data. Genes of interest can be input as Affymetrix probe identifiers, Genbank, or Unigene identifiers for human, mouse or rat genomes. Results are provided in a user friendly interface with hyperlinks to the sources of information.

Highlights

Microarrays are useful in profiling entire genomes of organisms under specific conditions [1]
The objective of this study was to develop a comprehensive tool to extract a wide range of annotative information from microarray data, and to provide this detailed information in a user friendly environment
GOAPhAR is an acronym for Gene Ontology, Annotation and Pathways for Array Research

Summary

Introduction

Microarrays are useful in profiling entire genomes of organisms under specific conditions [1]. Data generated are used to assess relationships among genes and to obtain a detailed understanding of underlying cellular processes. After the data are generated, probeset signals are filtered from noise and background. Normalization techniques [2] are applied to minimize technical variation and probe subsets are selected for detailed analysis. An initial step in analysis is to obtain annotative information for the selected probesets [3]. Annotation can include; structural information such as chromosome location, sequence information, coding regions, or homologs in other genomes; functional information such as biological pathways; and associated publications. Because of its vast and heterogeneous nature, these resources are scattered among many sites, and it can be a daunting task to locate relevant information from the disparate sources [4]

Objectives

Methods

Results