Question: Correlate phenotype and gene expression data
0
gravatar for S_B_P
21 months ago by
S_B_P0
S_B_P0 wrote:

I have experimental quantitative data of an immune phenotype (as a continuous variable) for 7 inbred mouse strains. From Immunological genome project immgen.org), I have obtained raw data for immune cell gene expression, from which I can calculate gene expression differences across any pair of mouse strains. From the 7 pairs of strains, I generate C(7,2) = 21 possible pairs. For each of the 21 pairs, I calculate the difference in phenotype (expressed as absolute difference or ratio). From the same set of 21 pairs I generate gene expression differences for each pair. How can I correlate the 21 'phenotype' measures and 21 'gene-expression' measures to come up with a potential list of genes that could be associated with the phenotype ? Is there a statistical method or gene set enrichment tool that can pick up quantitative differences in groups of gene sets such as this ?

ADD COMMENTlink modified 21 months ago by Jean-Karim Heriche18k • written 21 months ago by S_B_P0
3
gravatar for Jean-Karim Heriche
21 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

I don't see where you're going with computing all these pairs.
Identifying the genes contributing to the phenotype can be seen as a regression problem. You want to regress your phenotype Y on a linear combination of the gene levels Xi. See for example this paper. For this, you would use the strains as individuals.

ADD COMMENTlink written 21 months ago by Jean-Karim Heriche18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1668 users visited in the last hour