TY - GEN
T1 - Comparative genetic pathway analysis using structural equation Modeling
AU - Wu, Xiao
AU - Sharpe, Kathryn
AU - Zhang, Tianyi
AU - Chen, Hongyan
AU - Zhu, Wei
AU - Li, Ellen
AU - Taghavi, Safiyh
AU - Van Der Lelie, Daniel
PY - 2011
Y1 - 2011
N2 - In this work, we propose a novel genetic pathway discovery and comparison analysis framework integrating newly generated gene expression microarray data and existing biological pathway information. Starting with the significance analysis of microarray (SAM), a list of differentially expressed genes among groups is obtained. This gene list is then imported to the Ingenuity Pathway Analysis (IPA) to yield potentially relevant biological pathways. Finally, a newly-developed covariate structural equation modeling method is applied to evaluate gene-gene interactions and group difference. We illustrate this novel comparative pathway analysis pipeline using the whole human genome expression profiling data collected from a study of inflammatory bowel diseases (IBD) with 99 subjects from three phenotypic groups: ileal Crohn's disease (CD), ulcerative colitis (UC) and control non-IBD.
AB - In this work, we propose a novel genetic pathway discovery and comparison analysis framework integrating newly generated gene expression microarray data and existing biological pathway information. Starting with the significance analysis of microarray (SAM), a list of differentially expressed genes among groups is obtained. This gene list is then imported to the Ingenuity Pathway Analysis (IPA) to yield potentially relevant biological pathways. Finally, a newly-developed covariate structural equation modeling method is applied to evaluate gene-gene interactions and group difference. We illustrate this novel comparative pathway analysis pipeline using the whole human genome expression profiling data collected from a study of inflammatory bowel diseases (IBD) with 99 subjects from three phenotypic groups: ileal Crohn's disease (CD), ulcerative colitis (UC) and control non-IBD.
KW - Covariate Structural Equation Modeling
KW - Pathway Anlaysis
KW - Significance Analysis of Microarrays
UR - https://www.scopus.com/pages/publications/79953814026
U2 - 10.1109/ICCABS.2011.5729878
DO - 10.1109/ICCABS.2011.5729878
M3 - Conference contribution
AN - SCOPUS:79953814026
SN - 9781612848525
T3 - 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
SP - 190
EP - 195
BT - 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
T2 - 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011
Y2 - 3 February 2011 through 5 February 2011
ER -