title: Mouse proteome analysis.
abstract: A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein sequences derived from a nonredundant representative protein set (RPS) and a variant protein set (VPS) of the mouse transcriptome. The functional characterization and assignment of Gene Ontology terms was done by analysis of the proteome using InterPro. The Superfamily database analyses gave a detailed structural classification according to SCOP and provide additional evidence for the functional characterization of the proteome data. The MDS database analysis revealed new domains which are not presented in existing protein domain databases. Thus the transcriptome gives us a unique source of data for the detection of new functional groups. The data obtained for the RPS and VPS sets facilitated the comparison of different patterns of protein expression. A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteomes. The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins
authors.affiliation: EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK. alex@ebi.ac.uk
authors.forename: Alexander
authors.initials: A
authors.lastname: Kanapin
authors.forename: Serge
authors.initials: S
authors.lastname: Batalov
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Davis
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
authors.forename: Sean
authors.initials: S
authors.lastname: Grimmond
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Michele
authors.initials: M
authors.lastname: Magrane
authors.forename: Hideo
authors.initials: H
authors.lastname: Matsuda
authors.forename: Christian
authors.initials: C
authors.lastname: Schönbach
authors.forename: Rohan D
authors.initials: RD
authors.lastname: Teasdale
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yuan
mesh_terms: D000818:Animals; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000145:classification / Q000235:genetics; D030541:Databases, Genetic / Q000706:statistics & numerical data; D029721:Drosophila Proteins / Q000145:classification / Q000235:genetics; D004721:Endoplasmic Reticulum / Q000145:classification; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods / Q000706:statistics & numerical data; D006801:Humans; D008565:Membrane Proteins / Q000145:classification / Q000235:genetics; D051379:Mice; D011237:Predictive Value of Tests; D021382:Protein Sorting Signals / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D020543:Proteome / Q000145:classification / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000145:classification / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D008565:Membrane Proteins; D021382:Protein Sorting Signals; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins