Graph-based analysis and visualization of experimental results with ONDEX

Köhler J, Baumbach J, Taubert J, Specht M, Skusa A, Rüegg A, Rawlings C, Verrier P, Philippi S (2006)
Bioinformatics 22(11): 1383-1390.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Köhler, Jacob; Baumbach, Jan; Taubert, Jan; Specht, Michael; Skusa, Andre; Rüegg, Alexander; Rawlings, Chris; Verrier, Paul; Philippi, Stephan
Abstract / Bemerkung
Motivation: Assembling the relevant information needed to interpret the output from high-throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles). Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise. Results: This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function.
Erscheinungsjahr
2006
Zeitschriftentitel
Bioinformatics
Band
22
Ausgabe
11
Seite(n)
1383-1390
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/2499691

Zitieren

Köhler J, Baumbach J, Taubert J, et al. Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 2006;22(11):1383-1390.
Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rüegg, A., Rawlings, C., et al. (2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics, 22(11), 1383-1390. doi:10.1093/bioinformatics/bt081
Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rüegg, A., Rawlings, C., Verrier, P., and Philippi, S. (2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics 22, 1383-1390.
Köhler, J., et al., 2006. Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics, 22(11), p 1383-1390.
J. Köhler, et al., “Graph-based analysis and visualization of experimental results with ONDEX”, Bioinformatics, vol. 22, 2006, pp. 1383-1390.
Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rüegg, A., Rawlings, C., Verrier, P., Philippi, S.: Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 22, 1383-1390 (2006).
Köhler, Jacob, Baumbach, Jan, Taubert, Jan, Specht, Michael, Skusa, Andre, Rüegg, Alexander, Rawlings, Chris, Verrier, Paul, and Philippi, Stephan. “Graph-based analysis and visualization of experimental results with ONDEX”. Bioinformatics 22.11 (2006): 1383-1390.

77 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Interactive and coordinated visualization approaches for biological data analysis.
Cruz A, Arrais JP, Machado P., Brief Bioinform (), 2018
PMID: 29590305
Bipartite graphs in systems biology and medicine: a survey of methods and applications.
Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG., Gigascience 7(4), 2018
PMID: 29648623
KnetMaps: a BioJS component to visualize biological knowledge networks
Singh A, Rawlings CJ, Hassani-Pak K., 2018
PMID: PPR59092
KnetMaps: a BioJS component to visualize biological knowledge networks.
Singh A, Rawlings CJ, Hassani-Pak K., F1000Res 7(), 2018
PMID: 30755790
WebGIVI: a web-based gene enrichment analysis and visualization tool.
Sun L, Zhu Y, Mahmood ASMA, Tudor CO, Ren J, Vijay-Shanker K, Chen J, Schmidt CJ., BMC Bioinformatics 18(1), 2017
PMID: 28472919
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.
Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I., Adv Bioinformatics 2017(), 2017
PMID: 28804499
Mining integrated semantic networks for drug repositioning opportunities.
Mullen J, Cockell SJ, Tipney H, Woollard PM, Wipat A., PeerJ 4(), 2016
PMID: 26844016
Representing and querying disease networks using graph databases.
Lysenko A, Roznovăţ IA, Saqi M, Mazein A, Rawlings CJ, Auffray C., BioData Min 9(), 2016
PMID: 27462371
Developing integrated crop knowledge networks to advance candidate gene discovery.
Hassani-Pak K, Castellote M, Esch M, Hindle M, Lysenko A, Taubert J, Rawlings C., Appl Transl Genom 11(), 2016
PMID: 28018846
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine.
Castaneda C, Nalley K, Mannion C, Bhattacharyya P, Blake P, Pecora A, Goy A, Suh KS., J Clin Bioinforma 5(), 2015
PMID: 25834725
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I., Gigascience 4(), 2015
PMID: 26309733
ZoomOut: Analyzing Multiple Networks as Single Nodes.
Athanasiadis EI, Bourdakou MM, Spyrou GM., IEEE/ACM Trans Comput Biol Bioinform 12(5), 2015
PMID: 26451833
Data integration in biological research: an overview.
Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV., J Biol Res (Thessalon) 22(1), 2015
PMID: 26336651
Ondex Web: web-based visualization and exploration of heterogeneous biological networks.
Taubert J, Hassani-Pak K, Castells-Brooke N, Rawlings CJ., Bioinformatics 30(7), 2014
PMID: 24363379
Interactive exploration of integrated biological datasets using context-sensitive workflows.
Horn F, Rittweger M, Taubert J, Lysenko A, Rawlings C, Guthke R., Front Genet 5(), 2014
PMID: 24600467
Current advances in systems and integrative biology.
Robinson SW, Fernandes M, Husi H., Comput Struct Biotechnol J 11(18), 2014
PMID: 25379142
Mathematical and computational modeling in biology at multiple scales.
Tuszynski JA, Winter P, White D, Tseng CY, Sahu KK, Gentile F, Spasevska I, Omar SI, Nayebi N, Churchill CD, Klobukowski M, El-Magd RM., Theor Biol Med Model 11(), 2014
PMID: 25542608
Human diseases through the lens of network biology.
Furlong LI., Trends Genet 29(3), 2013
PMID: 23219555
Visualization of protein interaction networks: problems and solutions.
Agapito G, Guzzi PH, Cannataro M., BMC Bioinformatics 14 Suppl 1(), 2013
PMID: 23368786
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.
Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R., Pharmacol Ther 138(3), 2013
PMID: 23384594
The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.
Van Landeghem S, De Bodt S, Drebert ZJ, Inzé D, Van de Peer Y., Plant Cell 25(3), 2013
PMID: 23532071
dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts.
Vincent J, Dai Z, Ravel C, Choulet F, Mouzeyar S, Bouzidi MF, Agier M, Martre P., Database (Oxford) 2013(), 2013
PMID: 23660284
Tuning the dials of Synthetic Biology.
Arpino JA, Hancock EJ, Anderson J, Barahona M, Stan GB, Papachristodoulou A, Polizzi K., Microbiology 159(pt 7), 2013
PMID: 23704788
Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
Lysenko A, Urban M, Bennett L, Tsoka S, Janowska-Sejda E, Rawlings CJ, Hammond-Kosack KE, Saqi M., PLoS One 8(7), 2013
PMID: 23861834
Tools for managing and analyzing microarray data.
Koschmieder A, Zimmermann K, Trissl S, Stoltmann T, Leser U., Brief Bioinform 13(1), 2012
PMID: 21422065
Connecting the dots between PubMed abstracts.
Hossain MS, Gresock J, Edmonds Y, Helm R, Potts M, Ramakrishnan N., PLoS One 7(1), 2012
PMID: 22235301
IntegromeDB: an integrated system and biological search engine.
Baitaluk M, Kozhenkov S, Dubinina Y, Ponomarenko J., BMC Genomics 13(), 2012
PMID: 22260095
Exploring and linking biomedical resources through multidimensional semantic spaces.
Berlanga R, Jiménez-Ruiz E, Nebot V., BMC Bioinformatics 13 Suppl 1(), 2012
PMID: 22373409
Extending signaling pathways with protein-interaction networks. Application to apoptosis.
Planas-Iglesias J, Guney E, García-García J, Robertson KA, Raza S, Freeman TC, Ghazal P, Oliva B., OMICS 16(5), 2012
PMID: 22385281
Topological analysis and interactive visualization of biological networks and protein structures.
Doncheva NT, Assenov Y, Domingues FS, Albrecht M., Nat Protoc 7(4), 2012
PMID: 22422314
Bayesian integration of networks without gold standards.
Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ., Bioinformatics 28(11), 2012
PMID: 22492647
EnzML: multi-label prediction of enzyme classes using InterPro signatures.
De Ferrari L, Aitken S, van Hemert J, Goryanin I., BMC Bioinformatics 13(), 2012
PMID: 22533924
Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details.
Garcia-Garcia J, Bonet J, Guney E, Fornes O, Planas J, Oliva B., Mol Inform 31(5), 2012
PMID: 27477264
VANTED v2: a framework for systems biology applications.
Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, Czauderna T, Klukas C, Schreiber F., BMC Syst Biol 6(), 2012
PMID: 23140568
Muscle protein kinetics in cancer cachexia.
Johns N, Stephens NA, Preston T., Curr Opin Support Palliat Care 6(4), 2012
PMID: 23123817
Signalling network construction for modelling plant defence response.
Miljkovic D, Stare T, Mozetič I, Podpečan V, Petek M, Witek K, Dermastia M, Lavrač N, Gruden K., PLoS One 7(12), 2012
PMID: 23272172
Teaching the fundamentals of biological data integration using classroom games.
Schneider MV, Jimenez RC., PLoS Comput Biol 8(12), 2012
PMID: 23300402
Challenges in integrating Escherichia coli molecular biology data.
Lourenço A, Carneiro S, Rocha M, Ferreira EC, Rocha I., Brief Bioinform 12(2), 2011
PMID: 21059604
BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies.
Kozhenkov S, Sedova M, Dubinina Y, Gupta A, Ray A, Ponomarenko J, Baitaluk M., BMC Syst Biol 5(), 2011
PMID: 21235794
QAPgrid: a two level QAP-based approach for large-scale data analysis and visualization.
Inostroza-Ponta M, Berretta R, Moscato P., PLoS One 6(1), 2011
PMID: 21267077
Knowledge management for systems biology a general and visually driven framework applied to translational medicine.
Maier D, Kalus W, Wolff M, Kalko SG, Roca J, Marin de Mas I, Turan N, Cascante M, Falciani F, Hernandez M, Villà-Freixa J, Villà-Freixa J, Losko S., BMC Syst Biol 5(), 2011
PMID: 21375767
Customizable views on semantically integrated networks for systems biology.
Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein EM, Wilkinson D, Lydall D, Hallinan J, Wipat A., Bioinformatics 27(9), 2011
PMID: 21414991
Creating views on integrated multidomain data.
Rohn H, Klukas C, Schreiber F., Bioinformatics 27(13), 2011
PMID: 21551150
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis.
Lysenko A, Defoin-Platel M, Hassani-Pak K, Taubert J, Hodgman C, Rawlings CJ, Saqi M., BMC Bioinformatics 12(), 2011
PMID: 21612636
MGV: a generic graph viewer for comparative omics data.
Symons S, Nieselt K., Bioinformatics 27(16), 2011
PMID: 21666268
Literature mining, ontologies and information visualization for drug repurposing.
Andronis C, Sharma A, Virvilis V, Deftereos S, Persidis A., Brief Bioinform 12(4), 2011
PMID: 21712342
Medusa: A tool for exploring and clustering biological networks.
Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R, Aerts J., BMC Res Notes 4(), 2011
PMID: 21978489
SegMine workflows for semantic microarray data analysis in Orange4WS.
Podpečan V, Lavrač N, Mozetič I, Novak PK, Trajkovski I, Langohr L, Kulovesi K, Toivonen H, Petek M, Motaln H, Gruden K., BMC Bioinformatics 12(), 2011
PMID: 22029475
Comparative microbial modules resource: generation and visualization of multi-species biclusters.
Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R., PLoS Comput Biol 7(12), 2011
PMID: 22144874
Biana: a software framework for compiling biological interactions and analyzing networks.
Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B., BMC Bioinformatics 11(), 2010
PMID: 20105306
SBRML: a markup language for associating systems biology data with models.
Dada JO, Spasić I, Paton NW, Mendes P., Bioinformatics 26(7), 2010
PMID: 20176582
Visualization of omics data for systems biology.
Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC., Nat Methods 7(3 suppl), 2010
PMID: 20195258
Semantic integration of data on transcriptional regulation.
Baitaluk M, Ponomarenko J., Bioinformatics 26(13), 2010
PMID: 20427517
Biological knowledge management: the emerging role of the Semantic Web technologies.
Antezana E, Kuiper M, Mironov V., Brief Bioinform 10(4), 2009
PMID: 19457869
A flood of microbial genomes-do we need more?
Ahmed N., PLoS One 4(6), 2009
PMID: 19513110
Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases.
Lysenko A, Hindle MM, Taubert J, Saqi M, Rawlings CJ., Brief Bioinform 10(6), 2009
PMID: 19933213
PHI-base update: additions to the pathogen host interaction database.
Winnenburg R, Urban M, Beacham A, Baldwin TK, Holland S, Lindeberg M, Hansen H, Rawlings C, Hammond-Kosack KE, Köhler J., Nucleic Acids Res 36(database issue), 2008
PMID: 17942425
Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV., Plant Cell 20(6), 2008
PMID: 18591350
Integrative approaches for mining transcriptional regulatory programs in Arabidopsis.
Krishnan A, Pereira A., Brief Funct Genomic Proteomic 7(4), 2008
PMID: 18632743
Data curation + process curation=data integration + science.
Goble C, Stevens R, Hull D, Wolstencroft K, Lopez R., Brief Bioinform 9(6), 2008
PMID: 19060304
Arena3D: visualization of biological networks in 3D.
Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R., BMC Syst Biol 2(), 2008
PMID: 19040715
A survey of visualization tools for biological network analysis.
Pavlopoulos GA, Wegener AL, Schneider R., BioData Min 1(), 2008
PMID: 19040716
e-Science: relieving bottlenecks in large-scale genome analyses.
Craddock T, Harwood CR, Hallinan J, Wipat A., Nat Rev Microbiol 6(12), 2008
PMID: 19008893
CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.
Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A., J Biotechnol 129(2), 2007
PMID: 17229482
FlyMine: an integrated database for Drosophila and Anopheles genomics.
Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, Guillier F, Janssens H, Ji W, Mclaren P, North P, Rana D, Riley T, Sullivan J, Watkins X, Woodbridge M, Lilley K, Russell S, Ashburner M, Mizuguchi K, Micklem G., Genome Biol 8(7), 2007
PMID: 17615057
BNDB - the Biochemical Network Database.
Küntzer J, Backes C, Blum T, Gerasch A, Kaufmann M, Kohlbacher O, Lenhof HP., BMC Bioinformatics 8(), 2007
PMID: 17910766
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
PMID: 18034885
Quality control for terms and definitions in ontologies and taxonomies.
Köhler J, Munn K, Rüegg A, Skusa A, Smith B., BMC Bioinformatics 7(), 2006
PMID: 16623942
cPath: open source software for collecting, storing, and querying biological pathways.
Cerami EG, Bader GD, Gross BE, Sander C., BMC Bioinformatics 7(), 2006
PMID: 17101041

21 References

Daten bereitgestellt von Europe PubMed Central.

Osprey: a network visualization system.
Breitkreutz BJ, Stark C, Tyers M., Genome Biol. 4(3), 2003
PMID: 12620107
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.
Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R, Ozturk M., Bioinformatics 18(7), 2002
PMID: 12117798
Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension.
Doi A, Nagasaki M, Fujita S, Matsuno H, Miyano S., Appl. Bioinformatics 2(3), 2003
PMID: 15130807
Integration of data and methods for genome analysis.
Durand P, Medigue C, Morgat A, Vandenbrouck Y, Viari A, Rechenmann F., Curr Opin Drug Discov Devel 6(3), 2003
PMID: 12833667
Data integration and visualization system for enabling conceptual biology.
Gopalacharyulu PV, Lindfors E, Bounsaythip C, Kivioja T, Yetukuri L, Hollmen J, Oresic M., Bioinformatics 21 Suppl 1(), 2005
PMID: 15961455
KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173

AUTHOR UNKNOWN, DRUGS DISCOV TODAY BIOSILICO 2(), 2004

AUTHOR UNKNOWN, In Silico Biol. (Gedrukt) 5(), 2004
Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress.
Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF., Plant Physiol. 130(4), 2002
PMID: 12481097
PatternHunter: faster and more sensitive homology search.
Ma B, Tromp J, Li M., Bioinformatics 18(3), 2002
PMID: 11934743
AraCyc: a biochemical pathway database for Arabidopsis.
Mueller LA, Zhang P, Rhee SY., Plant Physiol. 132(2), 2003
PMID: 12805578

AUTHOR UNKNOWN, BSPP NEWSL 42(), 2002
Pathway studio--the analysis and navigation of molecular networks.
Nikitin A, Egorov S, Daraselia N, Mazo I., Bioinformatics 19(16), 2003
PMID: 14594725
Microarray analysis of nitric oxide responsive transcripts in Arabidopsis.
Parani M, Rudrabhatla S, Myers R, Weirich H, Smith B, Leaman DW, Goldman SL., Plant Biotechnol. J. 2(4), 2004
PMID: 17134397
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.
Remm M, Storm CE, Sonnhammer EL., J. Mol. Biol. 314(5), 2001
PMID: 11743721
BRENDA, the enzyme database: updates and major new developments.
Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681450
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
Integrating biological databases.
Stein LD., Nat. Rev. Genet. 4(5), 2003
PMID: 12728276
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M., Plant J. 37(6), 2004
PMID: 14996223
PHI-base: a new database for pathogen host interactions.
Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381911

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 16533819
PubMed | Europe PMC

Suchen in

Google Scholar