SWISS-PROT and 2D gel databases

Amos Bairoch BAIROCH at cmu.unige.ch
Thu Apr 29 04:58:52 EST 1993


SWISS-PROT and 2D gel databases

Two-dimensional (2D) gel techniques have made  enormous progress  in the last
few years. One of the consequences of this evolution has been the development
of databases that  contain master gels from a variety of mammalian tissues or
from bacterial sources.   These  databases  are going to play an increasingly
important role in the analysis of  genomes and of molecular diseases.  2D gel
databases  generally  contain  one  or  more  master  images of the gels that
correspond to the tissue  or  organism studied;  spots  on  these  images are
attributed an  identification  code  and a variable percentage of these spots 
are linked to known proteins. The  identification of a protein on a 2D gel is
generally carried out using antibodies or by microsequencing. Microsequencing
of 2D gel spots also produces partial sequences and physico-chemical data for
a number of yet uncharacterized proteins.

SWISS-PROT has committed itself to work in close collaboration  with a number
of groups developing 2D gel databases. Since last  year  cross-references are
already available to the gene-protein  database of Escherichia coli K-12 (now
called ECO2DBASE) [1] and  symmetrically  that  database  now contains cross-
references to SWISS-PROT.  As  a  second  step  we have expanded our links to
2D gel databases by integrating data from the following sources:

   - The Human 2D gel protein  database of the Faculty of Medicine of the
     University of Geneva (known as SWISS-2DPAGE). SWISS-2DPAGE currently
     contains data concerning plasma [2] and liver [3] proteins, but will
     soon include additional tissues.
   - The Human keratinocyte 2D gel protein database from the universities
     of Aarhus and Ghent [4] (known as AARHUS/GHENT-2DPAGE).

For both of these databases we provide:

  a) Cross-references (using the DR line) to the identificators for the spots
     corresponding to known or unknown microsequenced proteins.
  b) We have created new entries for microsequences that correspond to novel,
     yet unidentified, proteins [see the example in the appendix]. 
  c) In some cases  we  have  entered  the  extent  of the microsequences for
     already known proteins.  This  was  done  for proteins which are not yet
     well characterized. The availability of such  microsequences allows, for
     example, to confirm the position  of  a signal sequence cleavage site or
     to confirm the correctness of a translated genomic sequence.

In the near future  the collaboration with the group of D. Hochstrasser which
produces the  SWISS-2DPAGE database   will   be  expanded  in  the  following
directions:

  a) The MELANIE  software  package [5]  which  is a  complete system for the
     analysis of 2D  gels and which is developed by the group of Hochstrasser
     will allow its users to navigate back and forth between SWISS-2DPAGE and
     SWISS-PROT.

     For more information on Melanie, please contact Dr. Ron Appel:

       Email: appel at cih.hcuge.ch
       Tel: +41-22-372 62 64
       Fax: +41-22-372 61 98

  b) A file server  will  be  set  up  that  will allow anyone with a network
     connection to  obtain  annotated  graphic files containing the region of
     the gels that correspond to a selected SWISS-PROT entry linked to SWISS-
     2DPAGE.

[1] VanBogelen R.A., Sankar P., Clark R.L., Bogan J.A., Neidhardt F.C.
    Electrophoresis 13:1014-1054(1992).
[2] Hughes G.J., Frutiger S., Paquet N., Ravier F., Pasquali C.,
    Sanchez J.-C., James R., Tissot J.-D., Bjellqvist B.,Hochstrasser D.F.
    Electrophoresis 13:707-714(1992).
[3] Hochstrasser D.F., Frutiger S., Paquet N., Bairoch A., Ravier F.,
    Pasquali C., Sanchez J.-C., Tissot J.-D., Bjellqvist B., Vargas R.,
    Appel R.D., Hughes G.J.
    Electrophoresis 13:992-1001(1992).
[4] Celis J.E., Rasmussen H.H., Madsen P., Leffers H., Honore B., Dejgaard K.,
    Gesser  B., Olsen  E., Gromov P., Hoffmann H.J., Nielsen M., Celis A.,
    Basse B., Lauridsen J.B., Ratz G.P., Nielsen H., Andersen A.H., Walbum E.,
    Kjaergaard I., Puype M., Van Damme J., Vandekerckhove J.
    Electrophoresis 13:893-959(1992).
[5] Appel R., Hochstrasser D.F., Funk M., Vargas J.R., Pellegrini C.,
    Muller A.F., Scherrer J.-R.
    Electrophoresis 12:722-735(1991).


Appendix: example of a newly entered SWISS-PROT entry corresponding to a
          unknown liver protein in SWISS-2DPAGE.

ID   ULA1_HUMAN     STANDARD;      PRT;    10 AA.
AC   P30036;
DT   01-APR-1993 (REL. 25, CREATED)
DT   01-APR-1993 (REL. 25, LAST SEQUENCE UPDATE)
DT   01-APR-1993 (REL. 25, LAST ANNOTATION UPDATE)
DE   UNKNOWN PROTEIN FROM 2D-PAGE OF LIVER TISSUE (SPOT 2) (FRAGMENT).
OS   HOMO SAPIENS (HUMAN).
OC   EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA;
OC   EUTHERIA; PRIMATES.
RN   [1]
RP   SEQUENCE.
RC   TISSUE=LIVER;
RA   HOCHSTRASSER D.F., FRUTIGER S., PAQUET N., BAIROCH A., RAVIER F.,
RA   PASQUALI C., SANCHEZ J.-C., TISSOT J.-D., BJELLQVIST B., VARGAS R.,
RA   APPEL R.D., HUGHES G.J.;
RL   ELECTROPHORESIS 13:992-1001(1992).
CC   -!- ON THE 2D-GEL THE DETERMINED PI OF THIS UNKNOWN PROTEIN IS: 5.45,
CC       ITS MW IS: 70 KD.
DR   SWISS-2DPAGE; P30036; HUMAN.
FT   NON_TER       1      1
FT   NON_TER      10     10
SQ   SEQUENCE   10 AA;  965 MW;  515 CN;
     ASEAHXGAVN
//



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