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One question

Jeff Blanchard jlb at ncgr.org
Thu May 16 15:41:21 PDT 2002


Hello David,

GenMapp, GeneSpring, Spotfire and EcoCyc will do this to varying degrees.  We have developed a database/tool project that will do this as well.  Our focus is more towards toward capturing interactions in general and not on GIFS, although we do have KEGG maps in the database.  We have also implemented parts of the GO ontology into our schema.  As an example of what we can do

1.  Query the database to find all proteins involved in DNA repair or any GO term
2.  Get all interactions associated with those Proteins (or all canonical pathways, like KEGG Maps, associated with proteins)
3.  Automatically generate a graph from the interactions/pathways
4.  Synchronize graph with gene expression data through NCGR's ISYS

or 

you could start with a gene expression cluster visualized in ATV and build a graph of these genes in PathDB or get all pathways associated with the cluster.

As people in this mailing list understand, content is critical for this type of analysis.   In addition to KEGG and MIP data we have uploaded data from the papers below into our relational database.  We also have some hand curated Arabidopsis metabolism data.  In all we have over 50,000 interactions in yeast and Arabidopsis and many pathways.  We have also mapped the Affy Arabidopsis chip nomenclature to data our database.  We have a demo example using the Tepperman et al. 2000. PNAS data set.

We have an alpha version of PathDB 2.0 floating around and will have a full release in June.  Let me know if you are interested in an alpha version or learning more.

Cheers, Jeff

_____________________________________

Jeffrey L. Blanchard
Research Scientist, Computational Biology
National Center for Genome Resources
2935 Rodeo Park Dr.
Santa Fe, NM 87505
tel: 505-995-4405
----------------------------------------------------------------------
Adjunct Assistant Professor
Department of Molecular Genetics and Microbiology
University of New Mexico


----------------------------------------------------------------------------

The number of pairwise interactions is shown in parentheses.


Protein-Protein (Two-hybrid)
    (5390) Ito et al. 2000, 2001. Proc Natl Acad Sci U S A.
    (1572) Uetz et al. 2000. Nature. 
    
Protein-Protein Complex (TAP)
    (3397) Gavin et al. 2002. Nature.
    (4190) Ho et al. 2002. Nature.

Protein-DNA (Genome wide location analysis)
    (1248) Simon et al. 2001. Cell.
    (87) Ren et al. 2000. Science.

Protein-lipid (protein microarray)
    (433) Zhu et al. 2001. Science.

Synthetic Lethal
    (291) Tong et al. 2001. Science. 

Computational predictions
    (13166 from yeast) Mellor et al. 2002. Nucleic Acids Res.

Other Databases/Sources
    MIPS 
    KEGG
  ----- Original Message 
  ----- Original Message ----- 
  From: WATSON_DAVID_E at lilly.com 
  To: Michael Ashburner (Genetics) ; go-friends at genome.stanford.edu ; owner-gofriends at genome.stanford.edu ; pshannon at systemsbiology.org 
  Sent: Thursday, May 16, 2002 9:51 AM
  Subject: One question



  Does anyone know of software that can incorporate quantitative data on transcript or protein levels into a schematic of biochemical pathways. Example: Affy data into Kegg pathways. 

  If the answer is no, does anyone have suggestions on how to do this? 

  Thanks. 

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