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Literature DB >> 19816451

How to visually interpret biological data using networks.

Daniele Merico¹, David Gfeller, Gary D Bader.

Abstract

Networks in biology can appear complex and difficult to decipher. We illustrate how to interpret biological networks with the help of frequently used visualization and analysis patterns.

Entities: Gene Species

Mesh：

Year: 2009 PMID： 19816451 PMCID： PMC4154490 DOI： 10.1038/nbt.1567

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

18 in total

1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

Review 2. A genomic regulatory network for development.

Authors: Eric H Davidson; Jonathan P Rast; Paola Oliveri; Andrew Ransick; Cristina Calestani; Chiou-Hwa Yuh; Takuya Minokawa; Gabriele Amore; Veronica Hinman; Cesar Arenas-Mena; Ochan Otim; C Titus Brown; Carolina B Livi; Pei Yun Lee; Roger Revilla; Alistair G Rust; Zheng jun Pan; Maria J Schilstra; Peter J C Clarke; Maria I Arnone; Lee Rowen; R Andrew Cameron; David R McClay; Leroy Hood; Hamid Bolouri
Journal: Science Date: 2002-03-01 Impact factor: 47.728

3. Knowledge representation of signal transduction pathways.

Authors: K Fukuda; T Takagi
Journal: Bioinformatics Date: 2001-09 Impact factor: 6.937

4. A gene-coexpression network for global discovery of conserved genetic modules.

Authors: Joshua M Stuart; Eran Segal; Daphne Koller; Stuart K Kim
Journal: Science Date: 2003-08-21 Impact factor: 47.728

Review 5. A probabilistic view of gene function.

Authors: Andrew G Fraser; Edward M Marcotte
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6. The Systems Biology Graphical Notation.

Authors: Nicolas Le Novère; Michael Hucka; Huaiyu Mi; Stuart Moodie; Falk Schreiber; Anatoly Sorokin; Emek Demir; Katja Wegner; Mirit I Aladjem; Sarala M Wimalaratne; Frank T Bergman; Ralph Gauges; Peter Ghazal; Hideya Kawaji; Lu Li; Yukiko Matsuoka; Alice Villéger; Sarah E Boyd; Laurence Calzone; Melanie Courtot; Ugur Dogrusoz; Tom C Freeman; Akira Funahashi; Samik Ghosh; Akiya Jouraku; Sohyoung Kim; Fedor Kolpakov; Augustin Luna; Sven Sahle; Esther Schmidt; Steven Watterson; Guanming Wu; Igor Goryanin; Douglas B Kell; Chris Sander; Herbert Sauro; Jacky L Snoep; Kurt Kohn; Hiroaki Kitano
Journal: Nat Biotechnol Date: 2009-08-07 Impact factor: 54.908

7. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.

Authors: Kristin C Gunsalus; Hui Ge; Aaron J Schetter; Debra S Goldberg; Jing-Dong J Han; Tong Hao; Gabriel F Berriz; Nicolas Bertin; Jerry Huang; Ling-Shiang Chuang; Ning Li; Ramamurthy Mani; Anthony A Hyman; Birte Sönnichsen; Christophe J Echeverri; Frederick P Roth; Marc Vidal; Fabio Piano
Journal: Nature Date: 2005-08-11 Impact factor: 49.962

8. 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

9. BioGRID: a general repository for interaction datasets.

Authors: Chris Stark; Bobby-Joe Breitkreutz; Teresa Reguly; Lorrie Boucher; Ashton Breitkreutz; Mike Tyers
Journal: Nucleic Acids Res Date: 2006-01-01 Impact factor: 16.971

10. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.

Authors: Teresa Reguly; Ashton Breitkreutz; Lorrie Boucher; Bobby-Joe Breitkreutz; Nizar N Batada; Gary C Hon; Chad L Myers; Ainslie Parsons; Helena Friesen; Rose Oughtred; Amy Tong; Chris Stark; Yuen Ho; David Botstein; Brenda Andrews; Charles Boone; Olga G Troyanskya; Trey Ideker; Kara Dolinski; Mike Tyers
Journal: J Biol Date: 2006-06-08

34 in total

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2. Islet adaptation to obesity and insulin resistance in WNIN/GR-Ob rats.

Authors: Himadri Singh; Sireesha Ganneru; Venkata Malakapalli; Maniprabha Chalasani; Giridharan Nappanveettil; Ramesh R Bhonde; Vijayalakshmi Venkatesan
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Review 3. Extending biochemical databases by metabolomic surveys.

Authors: Oliver Fiehn; Dinesh K Barupal; Tobias Kind
Journal: J Biol Chem Date: 2011-05-12 Impact factor: 5.157

4. Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.

Authors: Shuchi Smita; Amit Katiyar; Sangram Keshari Lenka; Monika Dalal; Amish Kumar; Sanjeet Kumar Mahtha; Gitanjali Yadav; Viswanathan Chinnusamy; Dev Mani Pandey; Kailash Chander Bansal
Journal: Funct Integr Genomics Date: 2019-07-08 Impact factor: 3.410

5. Exploratory Gene Ontology Analysis with Interactive Visualization.

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Journal: Sci Rep Date: 2019-05-24 Impact factor: 4.379

6. Exploring the anti-proliferative activity of Pelargonium sidoides DC with in silico target identification and network pharmacology.

Authors: A S P Pereira; M J Bester; Z Apostolides
Journal: Mol Divers Date: 2017-09-18 Impact factor: 2.943