QTL resources

QTL collections
Query our QTL collection for multiple sclerosis (MS) rheumathoid arthritis (RA) and their animal models EAE [Mouse] CIA [Mouse] [Rat] and others	Access the QTL collection by disease or species.
These databases are linked to the Expressionview (below).
Expressionview
	Data from genetic linkage analysis (QTLs, susceptibility loci) and/or from gene expression profiling may be displayed on several karyotypes: EXPRESSIONview on human EXPRESSIONview on mouse EXPRESSIONview on rat
Intergenomic search for QTL consensuses
MS and EAE QTL Databases may be queried for intergenomic consensuses with our QTLview [Description] [Precomputed results (2290 KB)]
Map conversion tools
	Try conversions and global comparisons between different mapping systems for the human, mouse or rat CARTOGRAPHER If you are interested in this tool, you may also find these SNP plots helpful.
SNP selection
For an easier selection of SNPs: SNPselect This interface performs a number of selections from the EnsEMBL mart tables beyond the current capabilities of the Mart UI. Use the consensus loci of the QTLview tool above to search for SNPs in these areas. If you find this tool helpful, you may also want to have a look at the SNP finder applications at chip.org and Affymetrix.com. The only other tool known to us catering for the retrieval and filtering of frequency rates is Frequency Finger [uchicago.edu]. However it will not let you filter on the ratio of frequencies or allow for more than a single locus at a time.
Expression QTLs for mouse model (EAE) of Multiple Sclerosis
Orange Juice © 1995-2004 by Michael W. Davidson and The Florida State University.	The Illumina BeadChip system yielded expression data for murine lymph nodes of EAE mice 30 days post immunisation. The mice were genotyped and scored. The combination of these data yields QTL for the expression of 520 genes on the chip. A paper is in preparation, for further details please download a poster. Upon request we grant full access access to a database with all QTLs determined with R/qtl and pairwise interactions.
Related Publications G. Fischer, S.M. Ibrahim, G.A. Brockmann, J.Pahnke, E.Bartocci, H.J. Thiesen, P. Serrano-Fernández, S. Möller "Expressionview: Visualization of Quantitative Trait Loci and Gene Expression Data in EnsEMBL." Genome Biology 4(11):R77 (2003) Full paper C. Voigt, S. Möller, S.M. Ibrahim, P. Serrano-Fernàndez "Non-linear conversion between genetic and physical chromosomal distances" Oral presentation: Proceedings of the German Conference in Bioinformatics, Munich, 2003. Publication:Bioinformatics 2004, 20(12):1966-196. P. Serrano-Fernández, S.M. Ibrahim, H.J. Thiesen, U.K. Zettl, R. Gödde, J. Epplen, S. Möller "Intergenomic Consensus in Multifactorial Inheritance Loci: the Case of Multiple Sclerosis". in press. Steffen Möller, Dirk Koczan, Pablo Serrano-Fernández, Uwe K. Zettl, Hans-Jürgen Thiesen, Saleh M. Ibrahim "Selecting SNPs for association studies based on population frequencies: Generation of a novel interactive tool and its application to multiple sclerosis" In Silico Biol. 4, 0035 (2004). Möller S, Serrano-Fernández P, Watson M, Koczan D, Kotsikoris V, Kunz M, Blüggel M, Pahnke J, Illges H, Mikkat S, Thiesen H-J, Glocker MO, Zettl UK, Ibrahim SM (2004) "Predicting soluble variants of membrane proteins". (submitted). "The Library" Silkscreen print © 1978 by Jacob Lawrence King County Public Art Collection

 
 

The Bioinformatics group at the Proteome Center Rostock within the Institute of Immunology of at the University of Rostock