RT Journal
A1 Kanapin, Alexander
A1 Batalov, Serge
A1 Davis, Melissa J.
A1 Gough, Julian
A1 Grimmond, Sean
A1 Kawaji, Hideya
A1 Magrane, Michele
A1 Matsuda, Hideo
A1 Schönbach, Christian
A1 Teasdale, Rohan D.
A1 RIKEN GER Group
A1 GSL Members
A1 Yuan3, Zheng
T1 Mouse Proteome Analysis
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6b 
SP 1335 
OP 1344 
DO 10.1101/gr.978703 
UL http://genome.cshlp.org/content/13/6b/1335.abstract 
AB 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