Re: cell types, brain regions mentioned in gensat

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.

Query regions:
Cerebellum
Cerebral cortex
Hippocampal formation
Hippocampal region
Hypothalamus
Lateral septal complex
Medulla
Midbrain
Olfactory bulb
Pallidum
Pons
Retrohippocampal region
Striatum
Striatum ventral region
Striatum-like amygdalar nuclei
Thalamus

Fine Structures:
Anterodorsal nucleus
Area postrema
Dentate gyrus
Dorsal nucleus raphé
Facial motor nucleus
Field CA1, pyramidal layer
Field CA3, pyramidal layer
Hypoglossal nucleus
Inferior olivary complex
Locus ceruleus
Medial habenula
Motor nucleus of trigeminal
Nucleus ambiguus
Nucleus of the solitary tract
Pontine gray
Red Nucleus
Reticular nucleus of the thalamus
Substantia nigra, compact part
Subthalamic nucleus
Ventral tegmental area

Received on Friday, 2 March 2007 20:55:13 UTC