GUDMAP - A SEARCHABLE DATABASE OF GENE EXPRESSION IN THE MOUSE REPRODUCTIVE
SYSTEM

 Kylie Georgas*, Duncan R. Davidson, Jamie A. Davies, Bruce J. Aronow, Cathy
  L. Mendelsohn, S. Steven Potter, E. Michelle Southard-Smith, Pumin Zhang,
 Andrew P. McMahon, James L. Lessard, Kevin W. Gaido, Sean Grimmond*, Peter
                       A. Koopman*, Melissa H. Little*

     *Institute for Molecular Bioscience, The University of Queensland,
                             Brisbane, Australia

      The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is an
international consortium of laboratories working to provide  the  scientific
and medical community with tools to  facilitate  research  on  genitourinary
(GU)  tract  development.  Laboratories  examining  gene  expression  during
reproductive development  include  the  Gaido  (The  Hamner  Institutes  for
Health Sciences), Lessard (Cincinnati Childrens  Hospital  Medical  Center),
Grimmond,  Koopman,  Little  (The  University  of  Queensland)  and  McMahon
(Harvard  University)  laboratories.  The  aim  of   the   project   is   to
comprehensively examine gene expression in organs of the GU tract so  as  to
identify  unique  temporal  and   spatial   markers   of   each   anatomical
compartment. To facilitate this we have created  a  public  website  through
which the GUDMAP database can be searched for  genes  expressed  in  the  GU
tract (www.gudmap.org). The website provides rapid access  to  primary  data
in the form of annotated expression patterns from both  microarray  and  RNA
/in situ/ hybridization (ISH).  Other  GUDMAP  tools  available  include;  (i)
illustrated  tutorials  describing  GU  anatomy  and   organogenesis,   (ii)
genetically  engineered  mouse  strains   to   facilitate   functional   and
developmental studies, and (iii) the GUDMAP  Disease  Database.  The  GUDMAP
database is a public resource funded by the National Institutes  of  Health,
USA and has been designed not  only  for  biologists  but  also  clinicians,
bioinformaticians and the general public.
      Wholemount and  section  ISH  data  make  up  the  bulk  of  the  gene
expression entries  on  the  GUDMAP  database  and  over  6000  entries  are
currently available. ISH  entries  include  raw  data  images,  experimental
details (including probe/gene information) and a fully annotated  text-based
expression profile which is linked to a searchable  anatomical  ontology  of
the mouse urogenital system. Expression is examined in a range of  embryonic
reproductive  organs  including  ovary,  testis,  male/female   mesonephros,
genital tubercle and organs of the urinary system (bladder, ureter,  kidney)
at various stages (12.5-13.5dpc, 15.5dpc) and in the early urogenital  tract
(10.5dpc).
      GUDMAP microarray data currently consists of  23  experimental  series
including 214 different tissue samples from the mouse  GU  tract.   The  raw
data and annotated gene expression profiles can be searched on  the  website
and downloaded.  Reproductive system datasets include the  genital  tubercle
at E14 and 3 developmental stage series for ovary and testis (E11,  12,  14,
16, 18, P2) and epididymis  (E12,  14,  16,  18,  P2).  Renal/urinary  tract
microarray data is also available for kidney, bladder and ureter at  various
stages of development.
      The expression data (both ISH and microarray)  is  searchable  on  the
website not only by gene or gene function but also by anatomical  structure.
 An advanced Boolean query allows  users  to  further  refine  their  search
according to the stage expressed  or  specific  tissue  expression  pattern.
The analysis of GUDMAP expression data has recently identified  novel  genes
which show sex-specific  gonad  expression  in  the  embryonic  reproductive
system and has revealed  novel  domains  of  expression  in  the  developing
genital tubercle.
      Finally, the GUDMAP Disease Database currently contains two data sets;
998 disease  terms  obtained  from  OMIM  and  an  additional  data  set  of
Mammalian Phenotype terms mapped to OMIM entries linking  phenotypes,  genes
and diseases associated with the GU tract.
      The high quality gene expression data GUDMAP provides has  enabled  us
to create an atlas of the molecular and cellular anatomy  of  the  mouse  GU
tract.   Given  the  importance  of  the  GU  tract  for  human  health  and
reproduction, GUDMAP  provides  a  much  needed  resource  from  which  more
advanced scientific and clinical research will follow.