Home LiteratureArticle Details
PMID: 19798086 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Network visualization and analysis of gene expression data using BioLayout Express(3D).

Nature protocols ·Vol. 4 ·No. 10 ·2009-00-00 ·Pages 1535-50

Theocharidis A, van Dongen S, Enright AJ, Freeman TC

Abstract

Network analysis has an increasing role in our effort to understand the complexity of biological systems. This is because of our ability to generate large data sets, where the interaction or distance between biological components can be either measured experimentally or calculated. Here we describe the use of BioLayout Express(3D), an application that has been specifically designed for the integration, visualization and analysis of large network graphs derived from biological data. We describe the basic functionality of the program and its ability to display and cluster large graphs in two- and three-dimensional space, thereby rendering graphs in a highly interactive format. Although the program supports the import and display of various data formats, we provide a detailed protocol for one of its unique capabilities, the network analysis of gene expression data and a more general guide to the manipulation of graphs generated from various other data types.

MeSH Terms
Cluster Analysis Computational Biology Data Mining Gene Expression Profiling/methods Oligonucleotide Array Sequence Analysis Software
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Theocharidis Athanasios
The Roslin Institute, R(D)SVS, University of Edinburgh, Roslin BioCentre, Midlothian, Scotland, UK.
van Dongen Stjin
Enright Anton J
Freeman Tom C
References (24)
24 references, click to expand
  1. Construction, visualisation, and clustering of transcription networks from microarray expression data.
    PLoS Comput Biol. 2007 Oct;3(10):2032-42 PMID: 17967053
  2. Integration of biological networks and gene expression data using Cytoscape.
    Nat Protoc. 2007;2(10):2366-82 PMID: 17947979
  3. Towards multidimensional genome annotation.
    Nat Rev Genet. 2006 Feb;7(2):130-41 PMID: 16418748
  4. A gene atlas of the mouse and human protein-encoding transcriptomes.
    Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7 PMID: 15075390
  5. VANTED: a system for advanced data analysis and visualization in the context of biological networks.
    BMC Bioinformatics. 2006 Mar 06;7:109 PMID: 16519817
  6. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 PMID: 16199517
  7. Protein families and TRIBES in genome sequence space.
    Nucleic Acids Res. 2003 Aug 1;31(15):4632-8 PMID: 12888524
  8. PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.
    Bioinformatics. 2002 Jul;18(7):996-1003 PMID: 12117798
  9. A general framework for weighted gene co-expression network analysis.
    Stat Appl Genet Mol Biol. 2005;4:Article17 PMID: 16646834
  10. An efficient algorithm for large-scale detection of protein families.
    Nucleic Acids Res. 2002 Apr 1;30(7):1575-84 PMID: 11917018
  11. Systems biology: understanding cells.
    Nature. 2003 Aug 21;424(6951):883 PMID: 12931164
  12. Computational systems biology.
    Nature. 2002 Nov 14;420(6912):206-10 PMID: 12432404
  13. Coexpression analysis of human genes across many microarray data sets.
    Genome Res. 2004 Jun;14(6):1085-94 PMID: 15173114
  14. Barriers to progress in systems biology.
    Nature. 2005 Dec 22;438(7071):1079 PMID: 16371982
  15. Evaluation of clustering algorithms for protein-protein interaction networks.
    BMC Bioinformatics. 2006 Nov 06;7:488 PMID: 17087821
  16. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.
    Am J Hum Genet. 2006 Jun;78(6):1011-25 PMID: 16685651
  17. DAVID: Database for Annotation, Visualization, and Integrated Discovery.
    Genome Biol. 2003;4(5):P3 PMID: 12734009
  18. Integration of CellDesigner and SABIO-RK.
    In Silico Biol. 2007;7(2 Suppl):S81-90 PMID: 17822394
  19. A survey of visualization tools for biological network analysis.
    BioData Min. 2008 Nov 28;1:12 PMID: 19040716
  20. A gene expression map for Caenorhabditis elegans.
    Science. 2001 Sep 14;293(5537):2087-92 PMID: 11557892
  21. Tools for visually exploring biological networks.
    Bioinformatics. 2007 Oct 15;23(20):2651-9 PMID: 17720984
  22. OrthoMCL: identification of ortholog groups for eukaryotic genomes.
    Genome Res. 2003 Sep;13(9):2178-89 PMID: 12952885
  23. Arena3D: visualization of biological networks in 3D.
    BMC Syst Biol. 2008 Nov 28;2:104 PMID: 19040715
  24. A logic-based diagram of signalling pathways central to macrophage activation.
    BMC Syst Biol. 2008 Apr 23;2:36 PMID: 18433497
Article Info
Journal
Nature protocols
Abbr.
Nat Protoc
ISSN
1750-2799
DOI
10.1038/nprot.2009.177
Published
2009-00-00
Epub
2009-00-01
Pages
1535-50
Language
English
Region
England
NLM ID
101284307
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BBS/E/D/05191131 · United Kingdom
Wellcome Trust · GR077040RP · United Kingdom
Biotechnology and Biological Sciences Research Council · BB / F003722 / 1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/F003722/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/I001107/1 · United Kingdom
External Links
PubMed source DOI: 10.1038/nprot.2009.177 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2