Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases

Tianyi Zhang, Robert A. DeSimone, Hongyan Chen, Christina M. Hamm, Jeffrey Yuan, Qing Qing Gong, Steven R. Hunt, Themistocles Dassopoulos, Rodney D. Newberry, Daniel N. Frank, Charles E. Robertson, Norman R. Pace, Erica Sodergren, George Weinstock, Xiangmin Jiao, Wei Zhu, Ellen Li

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

Whole human genome (Agilent) expression profiling was conducted on disease-unaffected ileal RNA collected from the proximal margin of resected ileum from 47 ileal Crohn's disease (CD), 27 ulcerative colitis (UC) and 25 control patients without inflammatory bowel diseases (IBD). Cluster analysis combined with significance analysis of microarrays (SAM) and principal component analysis (PCA) and was used to reduce the data dimension to identify geneprobe clusters associated with early pathogenic changes in ileal CD and UC. Ingenuity Pathway Analysis (IPA) was used to identify the biological pathways associated with each cluster. We reduced the dimensions of the 26,765 gene probe set to 43 gene-probe clusters. Most of these clusters could be labeled as related to different biological pathways, such as Paneth cell antimicrobial peptides, the formation of organized lymphoid structures, or nuclear receptor signaling and xenobiotic metabolism. Molecular phylogenetic 16S rRNA sequence analysis was completed on 83 DNA samples from the same samples used to generate the gene expression profiles. We conducted an exploratory study to determine if the first principle component (PC1) of these clusters could be linked to specific phyla/subphyla taxa.

Original languageEnglish
Title of host publication2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
Pages220-225
Number of pages6
DOIs
StatePublished - Apr 14 2011
Event1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 - Orlando, FL, United States
Duration: Feb 3 2011Feb 5 2011

Publication series

Name2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011

Conference

Conference1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
CountryUnited States
CityOrlando, FL
Period02/3/1102/5/11

Keywords

  • 16S rRNA sequence analysis
  • Cluster analysis
  • Crohn's disease
  • Dimension reduction
  • Microarray
  • Ulcerative colitis

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