- From: Alan Ruttenberg <alanruttenberg@gmail.com>
- Date: Fri, 2 Mar 2007 15:54:18 -0500
- To: Kei Cheung <kei.cheung@yale.edu>
- Cc: June Kinoshita <junekino@media.mit.edu>, Donald Doherty <donald.doherty@brainstage.com>, Gwen Wong <wonglabow@verizon.net>, public-semweb-lifesci@w3.org
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