TY - GEN
T1 - Biological pathway inference using manifold embedding
AU - Rao, Arvind
AU - Hero, Alfred O.
N1 - Copyright:
Copyright 2011 Elsevier B.V., All rights reserved.
PY - 2011
Y1 - 2011
N2 - Disease occurs due to aberrant modulation of biological pathways. Identification of activated gene pathways from gene expression data is an important problem. In this work, we develop a framework identifying activated pathways that incorporates cellular location of the gene, using gene ontology databases, in addition to gene expression data. This information is combined using Laplacian Eigenmaps to co-embed these data into a low dimensional manifold. Model-based clustering is then performed to identify biologically relevant activated pathways in the gene expression data. We illustrate the effectiveness of our manifold embedding approach for the problem of extracting immune system pathways from a macrophage gene expression dataset [11].
AB - Disease occurs due to aberrant modulation of biological pathways. Identification of activated gene pathways from gene expression data is an important problem. In this work, we develop a framework identifying activated pathways that incorporates cellular location of the gene, using gene ontology databases, in addition to gene expression data. This information is combined using Laplacian Eigenmaps to co-embed these data into a low dimensional manifold. Model-based clustering is then performed to identify biologically relevant activated pathways in the gene expression data. We illustrate the effectiveness of our manifold embedding approach for the problem of extracting immune system pathways from a macrophage gene expression dataset [11].
KW - Laplacian eigenmaps
KW - functional data analysis (FDA)
KW - gene ontology (GO)
KW - heterogeneous data integration
KW - immune response
UR - http://www.scopus.com/inward/record.url?scp=80051610616&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=80051610616&partnerID=8YFLogxK
U2 - 10.1109/ICASSP.2011.5947727
DO - 10.1109/ICASSP.2011.5947727
M3 - Conference contribution
AN - SCOPUS:80051610616
SN - 9781457705397
T3 - ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
SP - 5992
EP - 5995
BT - 2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings
T2 - 36th IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011
Y2 - 22 May 2011 through 27 May 2011
ER -