New micro-array, new EST assembly, call for annotation

Charles Hauser chauser at duke.edu
Sat Nov 16 11:31:53 EST 2002


New micro-array, new EST assembly, call for annotation

    We are preparing a 'complete' microarray by adding approximately
6000 more genes to the existing 2876. This should be constructed within
the next 5 months. In the meantime, we will be printing an interim array
(version 1.1) which will have the same representation as on the first
array plus an additional couple hundred genes. This leaves us the
opportunity to add your favorite genes. 

    If you have genes that you would like to see added to the array,
please let us know. To determine if your genes are already on the
microarray, download the table Chip v1.0 Excel file and its comments
available at: http://www.biology.duke.edu/chlamy_genome/microarrays.html
. 
- If you have already identified the ACEs/contig that corresponds to
that gene in the current EST assembly (20020630), search for it on the
Chip v1.0 Excel file using the 'find' command. If genes that you are
interested in are not on the array, compile an Excel file with a list of
ACEs/contigs that you want added, each associated with an annotation
that should include gene name whenever possible. 
- If you have not yet identified your favorite gene in the current
assembly, you may want to wait for the new EST assembly to be available
on the web (3rd week of November). The new assembly should have
approximately 2,000 new contigs. The Chip v1.0 Excel file will then be
amended to allow you to search for the presence of contigs from the new
assembly. The selection of new genes for the version 1.1 chip will have
to be done by December 1, 2002. 

    One of the most difficult aspects of making a useful array and
database is to have good annotation. Even if you have no specific
request or don't plan to use the chip, we are desperate for the full
annotation of any gene that you may have identified in the database,
whether it is on the current chip or not. This annotation will be added
to the existing database, and a new searchable category, 'Gene Name',
will be added. This is a good opportunity to make sure that each newly
identified gene is given an appropriate name. If everyone in the
community helps a little it will make our job much easier, and
facilitate the future annotation of the genome. Where possible, please
relate your gene name to a homolog in another organism [e.g.
Arabidopsis, yeast, human, E. coli]. 

    Wherever possible, gene names in Chlamydomonas should follow the
style recommended by the Commission on Plant Gene Nomenclature. 
Preferred nomenclature for nuclear genes in Chlamydomonas:  
     3 letter root name 
     1st letter is uppercase 
     2nd and 3rd letters are lowercase 
This is followed by uppercase letter or numeral(s)   e.g. AtpC, Cox3,
Oda2, RbcS2, Rsp6.  Most journals follow the convention that gene names
are in italics, wherease the names of the corresponding proteins are not
italicized.  

    If anyone has comments or suggestions on the next generation arrays
please contact Arthur Grossman (arthur at andrew2.stanford.edu), Zhaoduo
Zhang (zhaoduo at andrew2.stanford.edu), Jeff Shrager
(jshrager at andrew2.stanford.edu) or Olivier Vallon
(vallon at andrew2.stanford.edu).  For gene annotation please contact
Elizabeth Harris (chlamy at duke.edu) or Charles Hauser (chauser at duke.edu).


Chlamydomonas microarray home page:
http://www.biology.duke.edu/chlamy_genome/microarrays.html

Chip v1.0 Excel file 
http://www.biology.duke.edu/chlamy_genome/Array/Chip_v1_0.xls 

Commission on Plant Gene Nomenclature: 
http://mbclserver.rutgers.edu/CPGN/




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