Tools for Visualization and Analysis of Molecular Networks, Pathways, and -omics Data

Overview

Journal Adv Appl Bioinform Chem

Publisher Dove Medical Press

Specialty Chemistry

Date 2015 Jun 18

PMID 26082651

Citations 26

Authors

Jose M Villaveces

Prasanna Koti

Bianca H Habermann

Affiliations

Soon will be listed here.

Abstract

Biological pathways have become the standard way to represent the coordinated reactions and actions of a series of molecules in a cell. A series of interconnected pathways is referred to as a biological network, which denotes a more holistic view on the entanglement of cellular reactions. Biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization. Here, we review a set of pathway and network visualization and analysis methods and take a look at potential future developments in the field.

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References

Guzman F, Almerao M, Korbes A, Loss-Morais G, Margis R . Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis. PLoS One. 2012; 7(11):e49811. PMC: 3499529. DOI: 10.1371/journal.pone.0049811. View

Joshi-Tope G, Gillespie M, Vastrik I, DEustachio P, Schmidt E, de Bono B . Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2004; 33(Database issue):D428-32. PMC: 540026. DOI: 10.1093/nar/gki072. View

Kutmon M, Lotia S, Evelo C, Pico A . WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Res. 2014; 3:152. PMC: 4168754. DOI: 10.12688/f1000research.4254.2. View

Bae J, Watson B . Developing and evaluating Quilts for the depiction of large layered graphs. IEEE Trans Vis Comput Graph. 2011; 17(12):2268-75. DOI: 10.1109/TVCG.2011.187. View

. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2009; 38(Database issue):D142-8. PMC: 2808944. DOI: 10.1093/nar/gkp846. View

Rojdestvenski I . Metabolic pathways in three dimensions. Bioinformatics. 2003; 19(18):2436-41. DOI: 10.1093/bioinformatics/btg342. View

van Iersel M, Kelder T, Pico A, Hanspers K, Coort S, Conklin B . Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008; 9:399. PMC: 2569944. DOI: 10.1186/1471-2105-9-399. View

Theocharidis A, van Dongen S, Enright A, Freeman T . Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc. 2009; 4(10):1535-50. DOI: 10.1038/nprot.2009.177. View

Babur O, Aksoy B, Rodchenkov I, Sumer S, Sander C, Demir E . Pattern search in BioPAX models. Bioinformatics. 2013; 30(1):139-40. PMC: 3866551. DOI: 10.1093/bioinformatics/btt539. View

10.

Schellenberger J, Que R, Fleming R, Thiele I, Orth J, Feist A . Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011; 6(9):1290-307. PMC: 3319681. DOI: 10.1038/nprot.2011.308. View

11.

Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher C . The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2013; 42(Database issue):D459-71. PMC: 3964957. DOI: 10.1093/nar/gkt1103. View

12.

Kandasamy K, Mohan S, Raju R, Keerthikumar S, Sameer Kumar G, Venugopal A . NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010; 11(1):R3. PMC: 2847715. DOI: 10.1186/gb-2010-11-1-r3. View

13.

Freeman T, Goldovsky L, Brosch M, van Dongen S, Maziere P, Grocock R . Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol. 2007; 3(10):2032-42. PMC: 2041979. DOI: 10.1371/journal.pcbi.0030206. View

14.

Villaveces J, Jimenez R, Habermann B . KEGGViewer, a BioJS component to visualize KEGG Pathways. F1000Res. 2014; 3:43. PMC: 3954160. DOI: 10.12688/f1000research.3-43.v1. View

15.

Gomez J, Garcia L, Salazar G, Villaveces J, Gore S, Garcia A . BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics. 2013; 29(8):1103-4. PMC: 3624812. DOI: 10.1093/bioinformatics/btt100. View

16.

DeJongh M, Bockstege B, Frybarger P, Hazekamp N, Kammeraad J, McGeehan T . CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED. Bioinformatics. 2012; 28(6):891-2. PMC: 3307106. DOI: 10.1093/bioinformatics/btr719. View

17.

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View

18.

Aranda B, Blankenburg H, Kerrien S, Brinkman F, Ceol A, Chautard E . PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011; 8(7):528-9. PMC: 3246345. DOI: 10.1038/nmeth.1637. View

19.

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn A, Vinod N . Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007; 5:44. PMC: 2189715. DOI: 10.1186/1741-7007-5-44. View

20.

Doncheva N, Assenov Y, Domingues F, Albrecht M . Topological analysis and interactive visualization of biological networks and protein structures. Nat Protoc. 2012; 7(4):670-85. DOI: 10.1038/nprot.2012.004. View