Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line

Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R. Van Brocklyn, Eric G. Bremer

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

Background: Sphingosine 1-phosphate (S1P), a lysophospholipid, is involved in various cellular processes such as migration, proliferation, and survival. To date, the impact of S1P on human glioblastoma is not fully understood. Particularly, the concerted role played by matrix metalloproteinases (MMP) and S1P in aggressive tumor behavior and angiogenesis remains to be elucidated. Results: To gain new insights in the effect of S1P on angiogenesis and invasion of this type of malignant tumor, we used microarrays to investigate the gene expression in glioblastoma as a response to S1P administration in vitro. We compared the expression profiles for the same cell lines under the influence of epidermal growth factor (EGF), an important growth factor. We found a set of 72 genes that are significantly differentially expressed as a unique response to S1P. Based on the result of mining full-text articles from 20 scientific journals in the field of cancer research published over a period of five years, we inferred gene-gene interaction networks for these 72 differentially expressed genes. Among the generated networks, we identified a particularly interesting one. It describes a cascading event, triggered by S1P, leading to the transactivation of MMP-9 via neuregulin-1 (NRG-1), vascular endothelial growth factor (VEGF), and the urokinase-type plasminogen activator (uPA). This interaction network has the potential to shed new light on our understanding of the role played by MMP-9 in invasive glioblastomas. Conclusion: Automated extraction of information from biological literature promises to play an increasingly important role in biological knowledge discovery. This is particularly true for high-throughput approaches, such as microarrays, and for combining and integrating data from different sources. Text mining may hold the key to unraveling previously unknown relationships between biological entities and could develop into an indispensable instrument in the process of formulating novel and potentially promising hypotheses.

Original languageEnglish
Article number373
JournalBMC Bioinformatics
Volume7
DOIs
Publication statusPublished - 2006 Aug 10
Externally publishedYes

Fingerprint

Sphingosines
Gene expression
Phosphates
Cells
Genes
Matrix Metalloproteinase 9
Microarrays
Tumors
Neuregulin-1
Lysophospholipids
Urokinase-Type Plasminogen Activator
sphingosine 1-phosphate
Matrix Metalloproteinases
Epidermal Growth Factor
Vascular Endothelial Growth Factor A
Data mining
Intercellular Signaling Peptides and Proteins
Throughput

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. / Natarajan, Jeyakumar; Berrar, Daniel; Dubitzky, Werner; Hack, Catherine; Zhang, Yonghong; DeSesa, Catherine; Van Brocklyn, James R.; Bremer, Eric G.

In: BMC Bioinformatics, Vol. 7, 373, 10.08.2006.

Research output: Contribution to journalArticle

Natarajan, Jeyakumar ; Berrar, Daniel ; Dubitzky, Werner ; Hack, Catherine ; Zhang, Yonghong ; DeSesa, Catherine ; Van Brocklyn, James R. ; Bremer, Eric G. / Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. In: BMC Bioinformatics. 2006 ; Vol. 7.
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abstract = "Background: Sphingosine 1-phosphate (S1P), a lysophospholipid, is involved in various cellular processes such as migration, proliferation, and survival. To date, the impact of S1P on human glioblastoma is not fully understood. Particularly, the concerted role played by matrix metalloproteinases (MMP) and S1P in aggressive tumor behavior and angiogenesis remains to be elucidated. Results: To gain new insights in the effect of S1P on angiogenesis and invasion of this type of malignant tumor, we used microarrays to investigate the gene expression in glioblastoma as a response to S1P administration in vitro. We compared the expression profiles for the same cell lines under the influence of epidermal growth factor (EGF), an important growth factor. We found a set of 72 genes that are significantly differentially expressed as a unique response to S1P. Based on the result of mining full-text articles from 20 scientific journals in the field of cancer research published over a period of five years, we inferred gene-gene interaction networks for these 72 differentially expressed genes. Among the generated networks, we identified a particularly interesting one. It describes a cascading event, triggered by S1P, leading to the transactivation of MMP-9 via neuregulin-1 (NRG-1), vascular endothelial growth factor (VEGF), and the urokinase-type plasminogen activator (uPA). This interaction network has the potential to shed new light on our understanding of the role played by MMP-9 in invasive glioblastomas. Conclusion: Automated extraction of information from biological literature promises to play an increasingly important role in biological knowledge discovery. This is particularly true for high-throughput approaches, such as microarrays, and for combining and integrating data from different sources. Text mining may hold the key to unraveling previously unknown relationships between biological entities and could develop into an indispensable instrument in the process of formulating novel and potentially promising hypotheses.",
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AU - Hack, Catherine

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