title: Conserved abundance and topological features in chromatin-remodeling protein interaction networks.
abstract: The study of conserved protein interaction networks seeks to better understand the evolution and regulation of protein interactions. Here, we present a quantitative proteomic analysis of 18 orthologous baits from three distinct chromatin-remodeling complexes in Saccharomyces cerevisiae and Homo sapiens. We demonstrate that abundance levels of orthologous proteins correlate strongly between the two organisms and both networks have highly similar topologies. We therefore used the protein abundances in one species to cross-predict missing protein abundance levels in the other species. Lastly, we identified a novel conserved low-abundance subnetwork further demonstrating the value of quantitative analysis of networks.
authors.affiliation: Stowers Institute for Medical Research, Kansas City, MO, USA.
authors.forename: Mihaela E
authors.initials: ME
authors.lastname: Sardiu
authors.affiliation: Stowers Institute for Medical Research, Kansas City, MO, USA.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Gilmore
authors.affiliation: Stowers Institute for Medical Research, Kansas City, MO, USA.
authors.forename: Brad D
authors.initials: BD
authors.lastname: Groppe
authors.affiliation: Ayasdi, Inc., Palo Alto, CA, USA.
authors.forename: Damir
authors.initials: D
authors.lastname: Herman
authors.affiliation: Idexx Laboratories, Westbrook, ME, USA.
authors.forename: Sreenivasa R
authors.initials: SR
authors.lastname: Ramisetty
authors.affiliation: College of Life Sciences Jilin University, Changchun, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Cai
authors.affiliation: College of Life Sciences Jilin University, Changchun, China.
authors.forename: Jingji
authors.initials: J
authors.lastname: Jin
authors.affiliation: Stowers Institute for Medical Research, Kansas City, MO, USA Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, MO, USA.
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Conaway
authors.affiliation: Stowers Institute for Medical Research, Kansas City, MO, USA Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, MO, USA.
authors.forename: Joan W
authors.initials: JW
authors.lastname: Conaway
authors.affiliation: Stowers Institute for Medical Research, Kansas City, MO, USA.
authors.forename: Laurence
authors.initials: L
authors.lastname: Florens
authors.affiliation: Stowers Institute for Medical Research, Kansas City, MO, USA Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, MO, USA mpw@stowers.org.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Washburn
mesh_terms: D000074183:ATPases Associated with Diverse Cellular Activities; D000251:Adenosine Triphosphatases / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly / Q000502:physiology*; D004265:DNA Helicases / Q000378:metabolism; D004268:DNA-Binding Proteins; D051548:Histone Acetyltransferases / Q000378:metabolism; D006801:Humans; D000074443:Lysine Acetyltransferase 5; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D040901:Proteomics / Q000379:methods; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; C483404:INO80 complex, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D051548:Histone Acetyltransferases; C098489:KAT5 protein, human; D000074443:Lysine Acetyltransferase 5; C504740:NuA4 protein, S cerevisiae; D000251:Adenosine Triphosphatases; C481261:Swr1 protein, S cerevisiae; D000074183:ATPases Associated with Diverse Cellular Activities; D004265:DNA Helicases; C524421:INO80 protein, human; C119652:SRCAP protein, human
keywords: human; multidimensional protein identification technology; quantitative proteomics; topological data analysis; yeast