- From: kc28 <kei.cheung@yale.edu>
- Date: Sat, 03 Mar 2007 20:01:47 -0500
- To: Alan Ruttenberg <alanruttenberg@gmail.com>
- Cc: June Kinoshita <junekino@media.mit.edu>, Donald Doherty <donald.doherty@brainstage.com>, Gwen Wong <wonglabow@verizon.net>, public-semweb-lifesci@w3.org
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. >
Received on Sunday, 4 March 2007 01:03:52 UTC