Java-based Application Framework for Visualization of Gene Regulatory Region Annotations

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2004 Jan 31

PMID 14751988

Citations 4

Authors

Hao Sun

Ramana V Davuluri

Affiliations

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Abstract

Motivation: The genome sequences of several organisms are either complete, or being sequenced. Each genome needs to be integrated with various types of annotations, e.g. locations of genes, promoters and other functional elements such as transcriptional regulatory elements. A robust application framework will be useful for developing web-based applications to visualize various genome annotations.

Results: We developed genome data visualization toolkit (GDVTK) as an application framework that consists of a set of data structures and core classes, using Java technology. GDVTK is a sound framework for developing web-based applications to present the gene regulatory region annotations in visual form. The current version of GDVTK consists of eight packages and 38 Java classes that are portable, reusable and extensible for plugging in new data sources and models. We implemented GDVTK for visualization of promoter annotations in Mammalian Promoter Database (MPromDb), a web-based gene-regulatory information server.

Availability: GDVTK is available under GNU general public license. Source code and software documentation can be found at the URL http://bioinformatics.med.ohio-state.edu/GDVTK.

Citing Articles

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.

Yilmaz A, Mejia-Guerra M, Kurz K, Liang X, Welch L, Grotewold E Nucleic Acids Res. 2010; 39(Database issue):D1118-22.

PMID: 21059685 PMC: 3013708. DOI: 10.1093/nar/gkq1120.

Information Visualization Techniques in Bioinformatics during the Postgenomic Era.

Tao Y, Liu Y, Friedman C, Lussier Y Drug Discov Today Biosilico. 2010; 2(6):237-245.

PMID: 20976032 PMC: 2957900. DOI: 10.1016/S1741-8364(04)02423-0.

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks.

Palaniswamy S, James S, Sun H, Lamb R, Davuluri R, Grotewold E Plant Physiol. 2006; 140(3):818-29.

PMID: 16524982 PMC: 1400579. DOI: 10.1104/pp.105.072280.

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

Sun H, Palaniswamy S, Pohar T, Jin V, Huang T, Davuluri R Nucleic Acids Res. 2005; 34(Database issue):D98-103.

PMID: 16381984 PMC: 1347458. DOI: 10.1093/nar/gkj096.