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Literature DB >> 20195258

Visualization of omics data for systems biology.

Nils Gehlenborg¹, Seán I O'Donoghue, Nitin S Baliga, Alexander Goesmann, Matthew A Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum, Anne-Claude Gavin.

Abstract

High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data. In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions.

Mesh：

Year: 2010 PMID： 20195258 DOI： 10.1038/nmeth.1436

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

112 in total

1. Integration of biological networks and gene expression data using Cytoscape.

Authors: Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal: Nat Protoc Date: 2007 Impact factor: 13.491

Review 2. Visualizing genomes: techniques and challenges.

Authors: Cydney B Nielsen; Michael Cantor; Inna Dubchak; David Gordon; Ting Wang
Journal: Nat Methods Date: 2010-02-25 Impact factor: 28.547

3. A generic algorithm for layout of biological networks.

Authors: Falk Schreiber; Tim Dwyer; Kim Marriott; Michael Wybrow
Journal: BMC Bioinformatics Date: 2009-11-12 Impact factor: 3.169

4. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

Authors: P T Spellman; G Sherlock; M Q Zhang; V R Iyer; K Anders; M B Eisen; P O Brown; D Botstein; B Futcher
Journal: Mol Biol Cell Date: 1998-12 Impact factor: 4.138

5. Visual exploration of three-dimensional gene expression using physical views and linked abstract views.

Authors: Gunther H Weber; Oliver Rübel; Min-Yu Huang; Angela H DePace; Charless C Fowlkes; Soile V E Keränen; Cris L Luengo Hendriks; Hans Hagen; David W Knowles; Jitendra Malik; Mark D Biggin; Bernd Hamann
Journal: IEEE/ACM Trans Comput Biol Bioinform Date: 2009 Apr-Jun Impact factor: 3.710

Review 6. RNA-Seq: a revolutionary tool for transcriptomics.

Authors: Zhong Wang; Mark Gerstein; Michael Snyder
Journal: Nat Rev Genet Date: 2009-01 Impact factor: 53.242

7. Graph-based analysis and visualization of experimental results with ONDEX.

Authors: Jacob Köhler; Jan Baumbach; Jan Taubert; Michael Specht; Andre Skusa; Alexander Rüegg; Chris Rawlings; Paul Verrier; Stephan Philippi
Journal: Bioinformatics Date: 2006-03-13 Impact factor: 6.937

8. SpectralNET--an application for spectral graph analysis and visualization.

Authors: Joshua J Forman; Paul A Clemons; Stuart L Schreiber; Stephen J Haggarty
Journal: BMC Bioinformatics Date: 2005-10-19 Impact factor: 3.169

9. An evaluation of human protein-protein interaction data in the public domain.

Authors: Suresh Mathivanan; Balamurugan Periaswamy; T K B Gandhi; Kumaran Kandasamy; Shubha Suresh; Riaz Mohmood; Y L Ramachandra; Akhilesh Pandey
Journal: BMC Bioinformatics Date: 2006-12-18 Impact factor: 3.169

10. Reactome knowledgebase of human biological pathways and processes.

Authors: Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft; Bernard de Bono; Phani Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alex Kanapin; Suzanna Lewis; Shahana Mahajan; Bruce May; Esther Schmidt; Imre Vastrik; Guanming Wu; Ewan Birney; Lincoln Stein; Peter D'Eustachio
Journal: Nucleic Acids Res Date: 2008-11-03 Impact factor: 16.971

190 in total

1. Graphery: interactive tutorials for biological network algorithms.

Authors: Heyuan Zeng; Jinbiao Zhang; Gabriel A Preising; Tobias Rubel; Pramesh Singh; Anna Ritz
Journal: Nucleic Acids Res Date: 2021-07-02 Impact factor: 16.971

2. gViz, a novel tool for the visualization of co-expression networks.

Authors: Raphaël Helaers; Eric Bareke; Bertrand De Meulder; Michael Pierre; Sophie Depiereux; Naji Habra; Eric Depiereux
Journal: BMC Res Notes Date: 2011-10-27

3. Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation.

Authors: Astrid Junker; Hendrik Rohn; Tobias Czauderna; Christian Klukas; Anja Hartmann; Falk Schreiber
Journal: Nat Protoc Date: 2012-03-01 Impact factor: 13.491

Review 4. Genome-wide approaches to schizophrenia.

Authors: Jubao Duan; Alan R Sanders; Pablo V Gejman
Journal: Brain Res Bull Date: 2010-04-28 Impact factor: 4.077

5. The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage.

Authors: Hector Ramos; Paul Shannon; Mi-Youn Brusniak; Ulrike Kusebauch; Robert L Moritz; Ruedi Aebersold
Journal: Proteomics Date: 2010-12-06 Impact factor: 3.984