title: Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.
abstract: Global protein expression profiling can potentially uncover perturbations associated with common forms of heart disease. We have used shotgun MS/MS to monitor the state of biological systems in cardiac tissue correlating with disease onset, cardiac insufficiency and progression to heart failure in a time-course mouse model of dilated cardiomyopathy. However, interpreting the functional significance of the hundreds of differentially expressed proteins has been challenging. Here, we utilize improved enrichment statistical methods and an extensive collection of functionally related gene sets, gaining a more comprehensive understanding of the progressive alterations associated with functional decline in dilated cardiomyopathy. We visualize the enrichment results as an Enrichment Map, where significant gene sets are grouped based on annotation similarity. This approach vastly simplifies the interpretation of the large number of enriched gene sets found. For pathways of specific interest, such as Apoptosis and the MAPK (mitogen-activated protein kinase) cascade, we performed a more detailed analysis of the underlying signaling network, including experimental validation of expression patterns.
authors.affiliation: Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada.
authors.forename: Ruth
authors.initials: R
authors.lastname: Isserlin
authors.forename: Daniele
authors.initials: D
authors.lastname: Merico
authors.forename: Rasoul
authors.initials: R
authors.lastname: Alikhani-Koupaei
authors.forename: Anthony
authors.initials: A
authors.lastname: Gramolini
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
mesh_terms: D000818:Animals; D017209:Apoptosis / Q000502:physiology*; D002311:Cardiomyopathy, Dilated / Q000188:drug therapy / Q000235:genetics / Q000503:physiopathology*; D053148:Caspase 3 / Q000502:physiology; D030562:Databases, Protein; D018260:Gelsolin / Q000502:physiology; D020869:Gene Expression Profiling; D020935:MAP Kinase Signaling System / Q000502:physiology*; D055432:Metabolomics; D051379:Mice; D011433:Propranolol / Q000627:therapeutic use; D040901:Proteomics / Q000379:methods; D049490:Systems Biology; D053719:Tandem Mass Spectrometry
chemical_list: D018260:Gelsolin; D011433:Propranolol; D053148:Caspase 3