Alan et al.,
In addition to mapping to brain regions, what seems to be also missing
is some kind of brain coordinates. I thought one major advanatage of
using Google Map is the ability to issue GIS-like queries. With this
type queries, one can potentially query something like finding expressed
genes for a given brain region and its neighbouring/adjacent regions.
While we are talking about gene expression, what seems to be also
logical to consider is whether some highly expressed genes correlate
with high abundance of pathological proteins (e.g., amyloid beta). Any
take from neuroscientists?
-Kei
Alan Ruttenberg wrote:
On Mar 2, 2007, at 1:56 PM, Kei Cheung wrote:
By reading the AD/PD use case, one of the questions has to do with
what genes are expressed in what regions of the brain (if such gene
expressions are localized to certain brain regions). I wonder what
Alan's currently working on can help address this type of question
(even though the kind of gene expression data is for the mouse --
perhaps we can find homologous genes for human). Also, I'd encourage
people to take look at what Bill Bug's Wiki page:
What I can do is add an orthology mapping. Probably from orthogene.
I can also scrape the Allen site for the following query they provide
Brain Region(see list below), Expression-level(low/high),Expression-
density(low/high), expression pattern(clustered/not clustered). =>
gene set
So this would be 16x2x2x2 = 128 different gene sets.
There is also their "Fine structure search" :
Fine structure annotation lists are genes that have high specificity
expression in particular brain regions or nuclei.
They provide these gene lists for a set of structures listed below
(fine structures).
This can lead us to a particular image, though I don't have a way yet
to identify which portion of the image corresponds to a particular
region or structure.