Graph-based analysis and visualization of experimental results with ONDEX

Jacob Köhler, Jan Baumbach, Jan Taubert, Michael Specht, Andre Skusa, Alexander Rüegg, Chris Rawlings, Paul Verrier, Stephan Philippi

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

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.
OriginalsprogEngelsk
TidsskriftBioinformatics
Vol/bind22
Udgave nummer11
Sider (fra-til)1383-90
Antal sider8
ISSN1367-4803
DOI
StatusUdgivet - 2006
Udgivet eksterntJa

Fingeraftryk

Databases
Literature
Informatics
Data Mining
Metabolic Networks and Pathways
Semantics

Citer dette

Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rüegg, A., ... Philippi, S. (2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics, 22(11), 1383-90. https://doi.org/10.1093/bioinformatics/btl081
Köhler, Jacob ; Baumbach, Jan ; Taubert, Jan ; Specht, Michael ; Skusa, Andre ; Rüegg, Alexander ; Rawlings, Chris ; Verrier, Paul ; Philippi, Stephan. / Graph-based analysis and visualization of experimental results with ONDEX. I: Bioinformatics. 2006 ; Bind 22, Nr. 11. s. 1383-90.
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title = "Graph-based analysis and visualization of experimental results with ONDEX",
abstract = "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.",
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Köhler, J, Baumbach, J, Taubert, J, Specht, M, Skusa, A, Rüegg, A, Rawlings, C, Verrier, P & Philippi, S 2006, 'Graph-based analysis and visualization of experimental results with ONDEX', Bioinformatics, bind 22, nr. 11, s. 1383-90. https://doi.org/10.1093/bioinformatics/btl081

Graph-based analysis and visualization of experimental results with ONDEX. / Köhler, Jacob; Baumbach, Jan; Taubert, Jan; Specht, Michael; Skusa, Andre; Rüegg, Alexander; Rawlings, Chris; Verrier, Paul; Philippi, Stephan.

I: Bioinformatics, Bind 22, Nr. 11, 2006, s. 1383-90.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Graph-based analysis and visualization of experimental results with ONDEX

AU - Köhler, Jacob

AU - Baumbach, Jan

AU - Taubert, Jan

AU - Specht, Michael

AU - Skusa, Andre

AU - Rüegg, Alexander

AU - Rawlings, Chris

AU - Verrier, Paul

AU - Philippi, Stephan

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/btl081

DO - 10.1093/bioinformatics/btl081

M3 - Journal article

C2 - 16533819

VL - 22

SP - 1383

EP - 1390

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

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ER -