I am looking at the GTex portal for significantly different expression of certain genes, within individual tissue types. Is this the same thing as saying that the gene has a significant normalized effect size associated with an eQTL in a tissue? (For instance: https://gtexportal.org/home/gene/PTEN#eQTLBlock)
I'm having trouble figuring out how the eQTL plays in, vs. SNP vs. plain old normalized transcript counts. I'm not sure why SNPs and variants come into play. Thank you!!
•
written
by
rattus8 •
1 answer
Differential gene expression is very different from an eQTLS gene (eGene) between tissues . They are completely different concepts. I would suggest to spend time in understanding an eQTL/eGene vs differential gene by reading literature.
PS: SNPs and variants (SNVs) are not very different.
Log in to answer this question.
-
Blog: Tools and Future of eQTL: Data Gathering and Application in Genetic Medicine
written by Novogene •
-
DEseq2 on expected counts
written by lyan125 •
-
How to do further funtional analysis of DEG KeggGet output list?
written by joana.maclean •
-
Too many differentially expressed genes in voom
written by rzm0015 •
-
Can/should you interpret non-significant genes that cluster into modules with WGCNA?
written by N15
-
The gene expression effect of eQTL variants in high LD
written by seta
-
Transcript vs. Gene TPM counts?
written by n,n
-
Significant but very small beta coefficients in Cox proportional hazards calculation (survival)
written by atakanekiz
-
TMM or TPM normalized counts for visualization?
written by sam.vanc70 •
-
Advice on how to best express this set of data (deals with Gene expression and RPKM values)
written by michael.c.wang •
