# GNF SymAtlas Expression Data 

## Overview

Novartis' GNF SymAtlas provides experimental microarray data for human,
mouse and rat tissues with a wide range of biological conditions and
pathologies.

Table 1 lists all the GNF datasets currently available on GEO. These
data sets include raw CEL files as well as processed expression values.

  ------------------------------------------------------------------------ --------------------------- ------------------ -----------------
  **GEO**                                                                  **Title**                   **Species**        **Platform(s)**

  [GSE96](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96)         2002 GeneAtlas Data Set     Human              HG-U95A

  [GSE97](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97)         2002 GeneAtlas Data Set     Mouse              MG-U74

  [GSE952](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE952)       2004 Rat GeneAtlas Data Set Rat                RG-U34A

  [GSE1133](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE1133)    2004 GeneAtlas Data Set     Human              HG-U133A

  [GPL1073](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GPL1073)    2004 GeneAtlas Data Set     Mouse              GNF1M (Custom)

  [GPL1074](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GPL1074)    2004 GeneAtlas Data Set     Human              GNF1H (Custom)

  [GSE10246](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10246)   2008 Mouse GeneAtlas V3     Mouse              MOE430V2
                                                                           data set                                       
  ------------------------------------------------------------------------ --------------------------- ------------------ -----------------

Table 1: GNF datasets available on GEO

## Technical Approach

The current caBIO domain model does not directly support microarray
experiment data. There is a class called Anomaly (Figure 1) which
documents irregularities in gene expression at a high level. Low level
expression data is more appropriate for inclusion in caArray. Once
analysis is done, summary data could be added to caBIO.

![](media/image1.wmf){width="5.458333333333333in"
height="3.670138888888889in"}

Figure 1: Current Gene Expression Model

Data may be downloaded from GEO in tab-delimited format through the use
of their website or APIs.

## Issues/Risks

The SymAtlas application will be retired in the future, to be replaced
by the new BioGPS. This should not affect caBIO because we will be using
the data alone, without relying on any frontend.

## Tasks

The tasks are the same as for any new data brought into caBIO:

1.  Domain modeling

2.  Data loading

## Estimated Level of Effort 

If it is assumed that the data will be process and summarized in some
way, roughly 2 months would be required to add the summarized data to
caBIO.

Database expert -- 1 month

Software Engineer -- 1 month

## References

[SymAtlas: Supplementary Material]{.underline}.
<http://wombat.gnf.org/suppl.html>

[Future of SymAtlas]{.underline}, August 21, 2008.
<http://biogps.blogspot.com/2008/08/future-of-symatlas.html>

Su, Andrew I., et al. [Large-scale analysis of the human and mouse
transcriptomes.]{.underline}
<http://www.pnas.org/content/99/7/4465.abstract>