Literature-based discovery of diabetes- and ROS-related targets.
Literature-based discovery of diabetes- and ROS-related targets.
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DOI：
10.1186/1755-8794-3-49
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发表时间：
2010-10-27
影响因子：
2.7
通讯作者：
Feldman EL
中科院分区：
文献类型：
--
作者：
Hur J;Sullivan KA;Schuyler AD;Hong Y;Pande M;States DJ;Jagadish HV;Feldman EL
活性氧（ROS）是多种疾病（包括糖尿病并发症）中细胞损伤的已知介质。尽管它很重要，但目前还没有与 ROS 相关的基因的综合数据库。我们展示通过文本挖掘技术从生物医学文献中收集的 ROS 和糖尿病相关目标（基因/蛋白质）。基于网络的文献挖掘工具 SciMiner 被应用于 PubMed 索引的 1,154 篇糖尿病和 ROS 生物医学论文，以识别相关目标。 ROS 糖尿病文献中过度代表性的目标是通过与随机选择的文献进行比较而获得的。在糖尿病和非糖尿病 DBA/2J 小鼠的背根神经节 (DRG) 中测量了从排名最高的 ROS 糖尿病组中选出的 9 个基因的表达水平，以评估文献来源的靶标在糖尿病神经病变发病机制中的生物学相关性。 SciMiner 从 1,154 篇生物医学论文中确定了 1,026 个 ROS 和糖尿病相关靶标 (http://jdrf.neurology.med.umich.edu/ROSDiabetes/)。与随机选择的文献相比，ROS 糖尿病文献中的 53 个目标明显过多。这些过度代表性的靶标包括众所周知的氧化应激反应成员，包括过氧化氢酶、NADPH 氧化酶家族和超氧化物歧化酶蛋白质家族。九个选定基因中的八个在糖尿病和非糖尿病小鼠之间表现出显着差异表达。对于六个基因，糖尿病中表达变化的方向与 DRG 中氧化应激的增强平行。文献挖掘从生物医学文献中汇编了 ROS 与糖尿病相关的靶点，并引导我们评估所选靶点在糖尿病神经病变发病机制中的生物学相关性。
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. 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. 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. 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.
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影响因子：
8.3
作者：
Kawase, M;Murakami, K;Chan, PH
通讯作者：
Chan, PH
影响因子：
3.7
作者：
Folli, Franco;Guzzi, Valeria;Fiorina, Paolo
通讯作者：
Fiorina, Paolo
影响因子：
--
作者：
Fisher, RA
通讯作者：
Fisher, RA
DOI：
10.1093/bioinformatics/btp049
发表时间：
2009-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Hur J;Schuyler AD;States DJ;Feldman EL
通讯作者：
Feldman EL
生物公约概述：生物学信息提取的批判性评估。
影响因子：
3
作者：
Hirschman L;Yeh A;Blaschke C;Valencia A
通讯作者：
Valencia A