PMID- 16381885
OWN - NLM
STAT- MEDLINE
DCOM- 20060228
LR  - 20220408
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 34
IP  - Database issue
DP  - 2006 Jan 1
TI  - From genomics to chemical genomics: new developments in KEGG.
PG  - D354-7
AB  - The increasing amount of genomic and molecular information is the basis for 
      understanding higher-order biological systems, such as the cell and the organism, 
      and their interactions with the environment, as well as for medical, industrial 
      and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) 
      provides a reference knowledge base for linking genomes to biological systems, 
      categorized as building blocks in the genomic space (KEGG GENES) and the chemical 
      space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction 
      networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added 
      to the KEGG suite of databases. This reflects our attempt to computerize 
      functional interpretations as part of the pathway reconstruction process based on 
      the hierarchically structured knowledge about the genomic, chemical and network 
      spaces. In accordance with the new chemical genomics initiatives, the scope of 
      KEGG LIGAND has been significantly expanded to cover both endogenous and 
      exogenous molecules. Specifically, RPAIR contains curated chemical structure 
      transformation patterns extracted from known enzymatic reactions, which would 
      enable analysis of genome-environment interactions, such as the prediction of new 
      reactions and new enzyme genes that would degrade new environmental compounds. 
      Additionally, drug information is now stored separately and linked to new KEGG 
      DRUG structure maps.
FAU - Kanehisa, Minoru
AU  - Kanehisa M
AD  - Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, 
      Kyoto 611-0011, Japan. kanehisa@kuicr.kyoto-u.ac.jp
FAU - Goto, Susumu
AU  - Goto S
FAU - Hattori, Masahiro
AU  - Hattori M
FAU - Aoki-Kinoshita, Kiyoko F
AU  - Aoki-Kinoshita KF
FAU - Itoh, Masumi
AU  - Itoh M
FAU - Kawashima, Shuichi
AU  - Kawashima S
FAU - Katayama, Toshiaki
AU  - Katayama T
FAU - Araki, Michihiro
AU  - Araki M
FAU - Hirakawa, Mika
AU  - Hirakawa M
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (Enzymes)
RN  - 0 (Ligands)
RN  - 0 (Pharmaceutical Preparations)
SB  - IM
MH  - *Biotransformation
MH  - Chemical Phenomena
MH  - *Chemistry
MH  - *Databases, Factual
MH  - *Databases, Genetic
MH  - Environment
MH  - Enzymes/chemistry/genetics
MH  - *Genomics
MH  - Humans
MH  - Internet
MH  - Ligands
MH  - Pharmaceutical Preparations/chemistry/classification
MH  - Signal Transduction
MH  - Systems Integration
MH  - User-Computer Interface
PMC - PMC1347464
EDAT- 2005/12/31 09:00
MHDA- 2006/03/01 09:00
PMCR- 2005/12/28
CRDT- 2005/12/31 09:00
PHST- 2005/12/31 09:00 [pubmed]
PHST- 2006/03/01 09:00 [medline]
PHST- 2005/12/31 09:00 [entrez]
PHST- 2005/12/28 00:00 [pmc-release]
AID - 34/suppl_1/D354 [pii]
AID - 10.1093/nar/gkj102 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7. doi: 10.1093/nar/gkj102.

PMID- 19199708
OWN - NLM
STAT- MEDLINE
DCOM- 20090710
LR  - 20231105
IS  - 1535-3893 (Print)
IS  - 1535-3907 (Electronic)
IS  - 1535-3893 (Linking)
VI  - 8
IP  - 3
DP  - 2009 Mar
TI  - Proteomic analysis of human parotid gland exosomes by multidimensional protein 
      identification technology (MudPIT).
PG  - 1304-14
LID - 10.1021/pr800658c [doi]
AB  - Human ductal saliva contributes over a thousand unique proteins to whole oral 
      fluids. The mechanism by which most of these proteins are secreted by salivary 
      glands remains to be determined. The present study used a mass 
      spectrometry-based, shotgun proteomics approach to explore the possibility that a 
      subset of the proteins found in saliva are derived from exosomes, membrane-bound 
      vesicles of endosomal origin within multivesicular endosomes. Using MudPIT 
      (multidimensional protein identification technology) mass spectrometry, we 
      catalogued 491 proteins in the exosome fraction of human parotid saliva. Many of 
      these proteins were previously observed in ductal saliva from parotid glands (265 
      proteins). Furthermore, 72 of the proteins in parotid exosomes overlap with those 
      previously identified as urinary exosome proteins, proteins which are also 
      frequently associated with exosomes from other tissues and cell types. Gene 
      Ontology (GO) and KEGG pathway analyses found that cytosolic proteins comprise 
      the largest category of proteins in parotid exosomes (43%), involved in such 
      processes as phosphatidylinositol signaling system, calcium signaling pathway, 
      inositol metabolism, protein export, and signal transduction, among others; 
      whereas the integral plasma membrane proteins and associated/peripheral plasma 
      membrane proteins (26%) were associated with extracellular matrix-receptor 
      interaction, epithelial cell signaling, T-cell and B-cell receptor signaling, 
      cytokine receptor interaction, and antigen processing and presentation, among 
      other biological functions. In addition, these putative saliva exosomal proteins 
      were linked to specific diseases (e.g., neurodegenerative disorders, prion 
      disease, cancers, type I and II diabetes). Consequently, parotid glands secrete 
      exosomes that reflect the metabolic and functional status of the gland and may 
      also carry informative protein markers useful in the diagnosis and treatment of 
      systemic diseases.
FAU - Gonzalez-Begne, Mireya
AU  - Gonzalez-Begne M
AD  - Center for Oral Biology, University of Rochester Medical Center, Rochester, New 
      York 14642, USA.
FAU - Lu, Bingwen
AU  - Lu B
FAU - Han, Xuemei
AU  - Han X
FAU - Hagen, Fred K
AU  - Hagen FK
FAU - Hand, Arthur R
AU  - Hand AR
FAU - Melvin, James E
AU  - Melvin JE
FAU - Yates, John R
AU  - Yates JR
LA  - eng
GR  - R01 DE09692/DE/NIDCR NIH HHS/United States
GR  - U01 DE016267/DE/NIDCR NIH HHS/United States
GR  - T32 DE07202/DE/NIDCR NIH HHS/United States
GR  - P41 RR011823/RR/NCRR NIH HHS/United States
GR  - R01 DE009692-13/DE/NIDCR NIH HHS/United States
GR  - UO1 DE016267/DE/NIDCR NIH HHS/United States
GR  - R01 DE08921/DE/NIDCR NIH HHS/United States
GR  - P41 RR011823-09/RR/NCRR NIH HHS/United States
GR  - R01 DE009692/DE/NIDCR NIH HHS/United States
GR  - R01 DE008921-14/DE/NIDCR NIH HHS/United States
GR  - U01 DE016267-04/DE/NIDCR NIH HHS/United States
GR  - R01 DE008921/DE/NIDCR NIH HHS/United States
GR  - T32 DE007202/DE/NIDCR NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - J Proteome Res
JT  - Journal of proteome research
JID - 101128775
RN  - 0 (Proteome)
SB  - IM
MH  - Endosomes/metabolism
MH  - Exosomes/*metabolism
MH  - Humans
MH  - Parotid Gland/*metabolism
MH  - Proteome/*metabolism
MH  - Saliva/*metabolism
PMC - PMC2693447
MID - NIHMS90020
EDAT- 2009/02/10 09:00
MHDA- 2009/07/11 09:00
PMCR- 2010/03/06
CRDT- 2009/02/10 09:00
PHST- 2009/02/10 09:00 [entrez]
PHST- 2009/02/10 09:00 [pubmed]
PHST- 2009/07/11 09:00 [medline]
PHST- 2010/03/06 00:00 [pmc-release]
AID - 10.1021/pr800658c [doi]
PST - ppublish
SO  - J Proteome Res. 2009 Mar;8(3):1304-14. doi: 10.1021/pr800658c.