Ideas and suggestions for *a* database

odile%FRCGM51.earn at uk.ac.earn-relay odile%FRCGM51.earn at uk.ac.earn-relay
Wed Sep 8 15:58:19 EST 1993


                               Yeast intergene Database (YIP)
                                       project
 
 
Dear yeast netters,
 
 
The discussion proposed by Francis O. comes very well...
 
> What would you like to see in a yeast database ?
 
The *ideal* situation will be to have only one complete database full of
all the informations we need about yeast genes, sequences, media
etc... The dream... but before to be there, it's a long way to go...;-)
So for me, the first step is _to construct specialized databases_.
As I thought that we missed of a database where are collected informations
concerning yeast genetic interactions, after a lot of discussions with a
lot of people (thanks to them, specially to D. Stillman, L. Riles, D.
Kaback, A.Petitjean, F. Ouellette,  P. Bucher, A. Kalogeropoulos), I tried
to begin in my domain, with my small hands (;-)..) a database concerning
interacting genes: the Yeast Intergene Database (YID) (see below). I know
that it is a hard work with many scientific, computer ...financial and
political problems... But let's go...  So I turn the occasion of this
general database discussion to send my project on the yeast net.
 
The essential problem to begin this database is to collect the maximum of
informations to do it the most complete: bibliography of course is
essential but also direct intervention of the yeast workers
concerning their own genes could be a good solution.
So you will find below a form looking like the EMBL form, that I propose
to fill if you are concerned by interacting genes. You will find also
what I call "interacting genes" and also more details on my project.
 
......So, the ball was well running in France and goes on....
 
Please, see below my Yeast Intergene Database project...it's
not to long to read..;-)
 
                          Best regards,
 
                          Odile Ozier-Kalogeropoulos
                       e-mail: Odile at FRCGM51.BITNET
 
 
 
_____________________________________________________________________
 
 
                   Yeast Intergene Database (YID)
 
 
Many investigators have identified new genes by synthetic lethal
interactions or by identifying multicopy suppessors which overcome a
mutant phenotype when cloned on a multicopy vector. These methods have
been useful in revealing duplicated genes, identifying unknown
relationships in cellular metabolism and in finding novel regulatory
networks.
 
Informations concerning these genetic informations  are very
dispersed in many publications and consequently difficult to use. I would
like to create a database of Saccharomyces cerevisae genes showing such
properties of complex genetic interactions. This database should prove to
be an interesting tool for many investigators studying gene regulation,
regulatory pathways, complex cellular systems, functional analysis of
unknown open reading frames, etc.
To be most useful, this database should be accessible to the entire
scientific community, and this is best achieved electronically by FTP.
 
To construct this database, I need to collect information about these
genes and their genetic interactions and this is the reason of my letter. If
you have informations about synthetic lethal interactions or more
generally about interacting genes,and you are interested by this database
please fill the form below and returning it to me by e-mail. I should
greatly appreciated your collaboration.
 
 
                                best regards,
 
 
                                Odile Ozier-Kalogeropoulos
 
 
 
 
my mailing address:      CGM/CNRS
                        91190 GIF SUR YVETTE
                        FRANCE
 
e-mail address:  Odile at FRCGM51.BITNET
                 Odile at CGMVAX.CGM.CNRS-GIF.FR
 
telephone:  33 1 69 82 31 61
Fax number: 33 1 69 07 55 39
 
 
 
=================================================================
 
 
FORM PLAN
 
I.  General information
II.  Description of the gene of interest
III. Description of interacting gene(s)
        A. First interacting gene
                1. Characteristics
                2.  Relationships between the gene of interest (II)
                    and the interacting gene
                3.  Citation information
 
        B. Second interacting gene
 
        C, D... Other interacting genes
 
=================================================================
 
Wherever possible, please use standard nomenclature to answer questions
concerning the genes. If a question is not applicable to your
genes, answer by writing N.A. in the appropriate space; if the information is
relevant but unknown, write a question mark (?).
For questions with [   ] , inscribe a X in the right [  ] to answer.
If new data become available which would make the database entry more
informative , I urge you to contact me. Thank you.
 
 
I. GENERAL INFORMATION
=================================================================
Your name
------------------------------------------------------------------------------
Institution
------------------------------------------------------------------------------
Address
------------------------------------------------------------------------------
e-mail address
------------------------------------------------------------------------------
Telephone
------------------------------------------------------------------------------
Fax number
 
 
II.  DESCRIPTION OF THE GENE OF INTEREST
=================================================================
 
gene name
------------------------------------------------------------------------------
cloned   yes [ ]     no [ ]
--------------------------------------------------------------------------
accession number (if sequenced)
---------------------------------------------------------------------------
gene product name
------------------------------------------------------------------------------
sector (metabolic pathway, cell cycle, secretion,...)
 
 
------------------------------------------------------------------------------
 
III. DESCRIPTION OF INTERACTING GENE (S)
=================================================================
 
If several genes have been found interacting with the gene of interest,
please copy the section III of this form, insert it at the end of the text
and fill out  this section  for each additional  gene (B, C, D....)
 
 
A. FIRST INTERACTING GENE:
 
1. CHARACTERISTICS
------------------------------------------------------------------------------
gene name
------------------------------------------------------------------------------
cloned    yes    [ ]        no  [ ]
---------------------------------------------------------------------------
accession number (if sequenced)
---------------------------------------------------------------------------
gene product name
------------------------------------------------------------------------------
sector (metabolic pathway, cycle cell, secretion...)
 
 
-----------------------------------------------------------------------------
 
2.  RELATIONSHIPS BETWEEN THE GENE OF INTEREST (II) AND THE
INTERACTING GENE (III. A.1)
 
The association of the mutated [  ] or knocked-out [  ] gene of interest
and the mutated [  ] or knocked-out [  ] interacting gene is lethal
(synthetic lethal genes) [  ]
shows a specific phenotype [   ]        What phenotype ?
others [   ]  Precise
 
------------------------------------------------------------------------------
The  mutant [  ] or knocked-out [  ] gene of interest is rescued by the
interacting gene when present on a centromeric plasmid [   ], a multicopy
plasmid [  ], a mutated gene [ ] ?
 
------------------------------------------------------------------------------
Other relationships between the gene of interest and the interacting gene
 
------------------------------------------------------------------------------
 
3.  CITATION INFORMATION
 
These data are  [  ] published  [ ] in press  [  ] submitted  [ ] in preparation
                [ ] no plans to publish
------------------------------------------------------------------------------
authors
 
------------------------------------------------------------------------------
title of paper
 
------------------------------------------------------------------------------
journal                                     volume, first-last pages, year
 
------------------------------------------------------------------------------
 
 
B.  SECOND INTERACTING GENE
 
 
Please, copy here the section III of the form if several genes have been found
interacting with the gene of interest and fill out this section for each
additional gene (B, C, D....)
 
 
 
 
 
 



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