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

doi:10.1109/ICCABS.2011.5729884

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 proceeding › Conference contribution › peer-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 language	English
Title of host publication	2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
Pages	220-225
Number of pages	6
DOIs	https://doi.org/10.1109/ICCABS.2011.5729884
State	Published - 2011
Event	1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 - Orlando, FL, United States Duration: Feb 3 2011 → Feb 5 2011

Publication series

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

Conference

Conference	1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
Country/Territory	United States
City	Orlando, FL
Period	02/3/11 → 02/5/11

Keywords

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

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10.1109/ICCABS.2011.5729884

Cite this

Zhang, T., DeSimone, R. A., Chen, H., Hamm, C. M., Yuan, J., Gong, Q. Q., Hunt, S. R., Dassopoulos, T., Newberry, R. D., Frank, D. N., Robertson, C. E., Pace, N. R., Sodergren, E., Weinstock, G., Jiao, X., Zhu, W., & Li, E. (2011). Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 (pp. 220-225). [5729884] (2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011). https://doi.org/10.1109/ICCABS.2011.5729884

Zhang, Tianyi ; DeSimone, Robert A. ; Chen, Hongyan et al. / Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011. 2011. pp. 220-225 (2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011).

@inproceedings{395b4f352d2d4cc6b744fe108d0ed94e,

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

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.",

keywords = "16S rRNA sequence analysis, Cluster analysis, Crohn's disease, Dimension reduction, Microarray, Ulcerative colitis",

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

year = "2011",

doi = "10.1109/ICCABS.2011.5729884",

language = "English",

isbn = "9781612848525",

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

pages = "220--225",

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

note = "1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011 ; Conference date: 03-02-2011 Through 05-02-2011",

}

Zhang, T, DeSimone, RA, Chen, H, Hamm, CM, Yuan, J, Gong, QQ, Hunt, SR, Dassopoulos, T, Newberry, RD, Frank, DN, Robertson, CE, Pace, NR, Sodergren, E, Weinstock, G, Jiao, X, Zhu, W & Li, E 2011, Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. in 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011., 5729884, 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, pp. 220-225, 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, United States, 02/3/11. https://doi.org/10.1109/ICCABS.2011.5729884

Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. / Zhang, Tianyi; DeSimone, Robert A.; Chen, Hongyan et al.
2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011. 2011. p. 220-225 5729884 (2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases

AU - Zhang, Tianyi

AU - DeSimone, Robert A.

AU - Chen, Hongyan

AU - Hamm, Christina M.

AU - Yuan, Jeffrey

AU - Gong, Qing Qing

AU - Hunt, Steven R.

AU - Dassopoulos, Themistocles

AU - Newberry, Rodney D.

AU - Frank, Daniel N.

AU - Robertson, Charles E.

AU - Pace, Norman R.

AU - Sodergren, Erica

AU - Weinstock, George

AU - Jiao, Xiangmin

AU - Zhu, Wei

AU - Li, Ellen

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

KW - 16S rRNA sequence analysis

KW - Cluster analysis

KW - Crohn's disease

KW - Dimension reduction

KW - Microarray

KW - Ulcerative colitis

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DO - 10.1109/ICCABS.2011.5729884

M3 - Conference contribution

AN - SCOPUS:79953807399

SN - 9781612848525

T3 - 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011

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

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ER -

Zhang T, DeSimone RA, Chen H, Hamm CM, Yuan J, Gong QQ et al. Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011. 2011. p. 220-225. 5729884. (2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011). doi: 10.1109/ICCABS.2011.5729884

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

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Keywords

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