Grange, Pascal, Mitra, Partha P (May 2012) Computational neuroanatomy and gene expression: optimal sets of marker genes for brain regions. (Submitted)
![[thumbnail of 1205.2721v1.pdf]](https://repository.cshl.edu/style/images/fileicons/application_pdf.png) |
PDF
1205.2721v1.pdf - Submitted Version Available under License Creative Commons Attribution Non-commercial No Derivatives. Download (166kB) |
Abstract
The three-dimensional data-driven Allen Gene Expression Atlas of the adult mouse brain consists of numerized in-situ hybridization data for thousands of genes, co-registered to the Allen Reference Atlas. We propose quantitative criteria to rank genes as markers of a brain region, based on the localization of the gene expression and on its functional fitting to the shape of the region. These criteria lead to natural generalizations to sets of genes. We find sets of genes weighted with coefficients of both signs with almost perfect localization in all major regions of the left hemisphere of the brain, except the pallidum. Generalization of the fitting criterion with positivity constraint provides a lesser improvement of the markers, but requires sparser sets of genes.
| Item Type: | Paper |
|---|---|
| Subjects: | Investigative techniques and equipment > brain atlas bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression neurobiology > neuroanatomy |
| CSHL Authors: | |
| Communities: | CSHL labs > Mitra lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 11 May 2012 |
| Date Deposited: | 13 Oct 2023 15:48 |
| Last Modified: | 13 Oct 2023 15:48 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/41247 |
Actions (login required)
 |
Administrator's edit/view item |
