Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis

Kushida, Tatsuya; Asanuma, Takao; Okuda, Yoshihiro; Shidahara, Yo; Takagi, Toshihisa

doi:10.1109/cisis.2009.79

Cited by 3 publications

(2 citation statements)

References 23 publications

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“…1 Outline of the computer-assisted text mining method used for the lactoferrin interaction extraction process examined the extraction errors of the interaction information obtained and all of the extraction errors were corrected or deleted manually. This combination of machine and manual curation is referred to as ''hybrid curation'' (Kushida et al 2009). …”

Section: Methodsmentioning

confidence: 99%

“…In order to overcome the information overload associated with lactoferrin, we applied a text mining method to the accumulated lactoferrin literature. To this end, we used the computer-assisted information extraction system GENPAC, which uses natural language processing and text mining technology (Kushida et al 2009). We applied this method to certain functions and diseases to determine the possible participation of lactoferrin.…”

Section: Introductionmentioning

confidence: 99%

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A preliminary approach to creating an overview of lactoferrin multi-functionality utilizing a text mining method

Shimazaki

Kushida²

2010

Biometals

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Lactoferrin is a multi-functional metal-binding glycoprotein that exhibits many biological functions of interest to many researchers from the fields of clinical medicine, dentistry, pharmacology, veterinary medicine, nutrition and milk science. To date, a number of academic reports concerning the biological activities of lactoferrin have been published and are easily accessible through public data repositories. However, as the literature is expanding daily, this presents challenges in understanding the larger picture of lactoferrin function and mechanisms. In order to overcome the "analysis paralysis" associated with lactoferrin information, we attempted to apply a text mining method to the accumulated lactoferrin literature. To this end, we used the information extraction system GENPAC (provided by Nalapro Technologies Inc., Tokyo). This information extraction system uses natural language processing and text mining technology. This system analyzes the sentences and titles from abstracts stored in the PubMed database, and can automatically extract binary relations that consist of interactions between genes/proteins, chemicals and diseases/functions. We expect that such information visualization analysis will be useful in determining novel relationships among a multitude of lactoferrin functions and mechanisms. We have demonstrated the utilization of this method to find pathways of lactoferrin participation in neovascularization, Helicobacter pylori attack on gastric mucosa, atopic dermatitis and lipid metabolism.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A preliminary approach to creating an overview of lactoferrin multi-functionality utilizing a text mining method

Shimazaki

Kushida²

2010

Biometals

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IQGAP1 and vimentin are key regulator genes in naturally occurring hepatotumorigenesis induced by oxidative stress

Tsubota¹,

Matsumoto

Mogushi

et al. 2009

Carcinogenesis

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To identify key genes involved in the complex multistep process of hepatotumorigenesis, we reduced multivariate clinicopathological variables by using the Long-Evans Cinnamon rat, a model with naturally occurring and oxidative stress-induced hepatotumorigenesis. Gene expression patterns were analyzed serially by profiling liver tissues from rats of a naive status (4 weeks old), through to those with chronic hepatitis (26 and 39 weeks old) to tumor development (67 weeks old). Of 31 099 probe sets used for microarray analysis, 87 were identified as being upregulated in a stepwise manner during disease progression and tumor development. Quantitative real-time reverse transcription-polymerase chain reaction and statistical analyses verified that IQGAP1 and vimentin mRNA expression levels increased significantly throughout hepatotumorigenesis. A hierarchical clustering algorithm showed both genes clustered together and in the same cluster group. Immunohistochemical and western blot analyses showed similar increases in protein levels of IAGAP1 and vimentin. Finally, pathway analyses using text-mining technology with more comprehensive and recent gene-gene interaction data identified IQGAP1 and vimentin as important nodes in underlying gene regulatory networks. These findings enhance our understanding of the multistep hepatotumorigenesis and identification of target molecules for novel treatments.

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A syntactic rule-based method for automatic pathway information extraction from biomédical literature

Wang

Yang

Lin

et al. 2012

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops

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Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis

Cited by 3 publications

References 23 publications

A preliminary approach to creating an overview of lactoferrin multi-functionality utilizing a text mining method

A preliminary approach to creating an overview of lactoferrin multi-functionality utilizing a text mining method

IQGAP1 and vimentin are key regulator genes in naturally occurring hepatotumorigenesis induced by oxidative stress

A syntactic rule-based method for automatic pathway information extraction from biomédical literature

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Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis

Cited by 3 publications

References 23 publications

A preliminary approach to creating an overview of lactoferrin multi-functionality utilizing a text mining method

A preliminary approach to creating an overview of lactoferrin multi-functionality utilizing a text mining method

IQGAP1 and vimentin are key regulator genes in naturally occurring hepatotumorigenesis induced by oxidative stress

A syntactic rule-based method for automatic pathway information extraction from biom&#x00E9;dical literature

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A syntactic rule-based method for automatic pathway information extraction from biomédical literature