title: Differential protein network analysis of the immune cell lineage.
abstract: Recently, the Immunological Genome Project (ImmGen) completed the first phase of the goal to understand the molecular circuitry underlying the immune cell lineage in mice. That milestone resulted in the creation of the most comprehensive collection of gene expression profiles in the immune cell lineage in any model organism of human disease. There is now a requisite to examine this resource using bioinformatics integration with other molecular information, with the aim of gaining deeper insights into the underlying processes that characterize this immune cell lineage. We present here a bioinformatics approach to study differential protein interaction mechanisms across the entire immune cell lineage, achieved using affinity propagation applied to a protein interaction network similarity matrix. We demonstrate that the integration of protein interaction networks with the most comprehensive database of gene expression profiles of the immune cells can be used to generate hypotheses into the underlying mechanisms governing the differentiation and the differential functional activity across the immune cell lineage. This approach may not only serve as a hypothesis engine to derive understanding of differentiation and mechanisms across the immune cell lineage, but also help identify possible immune lineage specific and common lineage mechanism in the cells protein networks.
authors.affiliation: Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway.
authors.forename: Trevor
authors.identifier: 0000-0001-9896-0613
authors.initials: T
authors.lastname: Clancy
authors.affiliation: Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway ; Biomedical Research Group, Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, 0310 Oslo, Norway ; Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway.
authors.forename: Eivind
authors.initials: E
authors.lastname: Hovig
mesh_terms: D000818:Animals; D019070:Cell Lineage; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D007962:Leukocytes / Q000166:cytology* / Q000378:metabolism*; D051379:Mice; D060066:Protein Interaction Maps; D015534:Trans-Activators / Q000378:metabolism; D059467:Transcriptome
chemical_list: D015534:Trans-Activators