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J Theor Biol. 2014 Aug 7;354:48-53. doi: 10.1016/j.jtbi.2014.03.026. Epub 2014 Mar 24.

TIBS: a web database to browse gene expression in irritable bowel syndrome.

Author information

  • 1Institute of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210046, Jiangsu, People Republic of China. Electronic address: yanjing0513@126.com.
  • 2Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa 33612, USA. Electronic address: yxu@mail.usf.edu.
  • 3Essenology Software Inc., Wuxi 214187, People Republic of China. Electronic address: brianwhu@yahoo.com.
  • 4Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne 50674, Germany. Electronic address: salnajm@smail.uni-koeln.de.
  • 5Institute of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210046, Jiangsu, People Republic of China. Electronic address: lina_liu606@126.com.
  • 6Department of Pharmacology, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210046, People Republic of China. Electronic address: profyinlu@163.com.
  • 7Institute of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210046, Jiangsu, People Republic of China. Electronic address: pr_zhiguangsun@163.com.
  • 8Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa 33612, USA; Department of Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, Tampa 33612, USA. Electronic address: fcheng1@health.usf.edu.

Abstract

Irritable bowel syndrome (IBS) is a chronic functional gastrointestinal disorder. Its symptoms include chronic abdominal pain, bloating gas, diarrhea and constipation. Many IBS patients also have psychological symptoms like depression or anxiety. These unpleasant symptoms significantly lower patients׳ quality of life. The prevalence of IBS in Europe and North America is about 10-15% of the population, which makes IBS a disorder with a high social cost. The pathophysiology of IBS is considered to be multifactorial and the exact cause of the disease remains poorly understood. Recently, a genome-wide expression microarray technique has been applied to investigate the possible mechanisms of IBS. However, a user-friendly database that allows scientists without bioinformatics background to query gene expression levels in these data sets and compare gene expression patterns across different tissues has not yet been established. Therefore, we have integrated four public expression microarray data (320 samples) from the Gene Expression Omnibus (GEO) and ArrayExpress databases into an online database called Transcriptome of Irritable Bowel Syndrome (TIBS). The gene expression change in IBS patients compared to healthy volunteers or UC patients in jejunum, sigmoid colon, rectum, and descending colon can be queried by gene symbols. Users can compare gene expression levels of IBS patients across these tissues. Sex difference of gene expression in IBS patients was also shown in the database. The current version of TIBS database contains 42,400 annotated gene probe sets represented on the Affymetrix Human Genome U133 plus 2.0 platform. TIBS will be an invaluable resource for a better understanding of the pathogenesis of IBS at the molecular level and for drug development. The TIBS database is available online at http://www.chengfeng.info/tibs_database.html.

Copyright © 2014 Elsevier Ltd. All rights reserved.

KEYWORDS:

Bioinformatics; IBS; Microarray; Online server; Ulcerative colitis

PMID:
24675620
[PubMed - in process]
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