Literature-based discovery of diabetes- and ROS-related targets

Junguk Hur, Kelli A. Sullivan, Adam D. Schuyler, Yu Hong, Manjusha Pande, David J. States, H. V. Jagadish, Eva L. Feldman

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Background. Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS. Methods. We present ROS- and diabetes-related targets (genes/proteins) collected from the biomedical literature through a text mining technology. A web-based literature mining tool, SciMiner, was applied to 1,154 biomedical papers indexed with diabetes and ROS by PubMed to identify relevant targets. Over-represented targets in the ROS-diabetes literature were obtained through comparisons against randomly selected literature. The expression levels of nine genes, selected from the top ranked ROS-diabetes set, were measured in the dorsal root ganglia (DRG) of diabetic and non-diabetic DBA/2J mice in order to evaluate the biological relevance of literature-derived targets in the pathogenesis of diabetic neuropathy. Results. SciMiner identified 1,026 ROS- and diabetes-related targets from the 1,154 biomedical papers (http://jdrf. neurology.med.umich.edu/ROSDiabetes/). Fifty-three targets were significantly over-represented in the ROS-diabetes literature compared to randomly selected literature. These over-represented targets included well-known members of the oxidative stress response including catalase, the NADPH oxidase family, and the superoxide dismutase family of proteins. Eight of the nine selected genes exhibited significant differential expression between diabetic and non-diabetic mice. For six genes, the direction of expression change in diabetes paralleled enhanced oxidative stress in the DRG. Conclusions. Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the pathogenesis of diabetic neuropathy.

Original languageEnglish (US)
Article number49
JournalBMC Medical Genomics
Volume3
DOIs
StatePublished - Oct 29 2010

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Literature Based Discovery
Reactive Oxygen Species
Diabetic Neuropathies
Spinal Ganglia
Oxidative Stress
Genes
Inbred DBA Mouse
Data Mining
NADPH Oxidase
Diabetes Complications
Neurology
PubMed
Catalase
Superoxide Dismutase

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

Hur, J., Sullivan, K. A., Schuyler, A. D., Hong, Y., Pande, M., States, D. J., ... Feldman, E. L. (2010). Literature-based discovery of diabetes- and ROS-related targets. BMC Medical Genomics, 3, [49]. https://doi.org/10.1186/1755-8794-3-49

Literature-based discovery of diabetes- and ROS-related targets. / Hur, Junguk; Sullivan, Kelli A.; Schuyler, Adam D.; Hong, Yu; Pande, Manjusha; States, David J.; Jagadish, H. V.; Feldman, Eva L.

In: BMC Medical Genomics, Vol. 3, 49, 29.10.2010.

Research output: Contribution to journalArticle

Hur, J, Sullivan, KA, Schuyler, AD, Hong, Y, Pande, M, States, DJ, Jagadish, HV & Feldman, EL 2010, 'Literature-based discovery of diabetes- and ROS-related targets', BMC Medical Genomics, vol. 3, 49. https://doi.org/10.1186/1755-8794-3-49
Hur J, Sullivan KA, Schuyler AD, Hong Y, Pande M, States DJ et al. Literature-based discovery of diabetes- and ROS-related targets. BMC Medical Genomics. 2010 Oct 29;3. 49. https://doi.org/10.1186/1755-8794-3-49
Hur, Junguk ; Sullivan, Kelli A. ; Schuyler, Adam D. ; Hong, Yu ; Pande, Manjusha ; States, David J. ; Jagadish, H. V. ; Feldman, Eva L. / Literature-based discovery of diabetes- and ROS-related targets. In: BMC Medical Genomics. 2010 ; Vol. 3.
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