DESCRIPTION:
All independent cis-eQTLs that were identified in RNA from 51 eye samples, for GWAS for intraocular pressure (IOP), that is, conditionally independent cis-eQTLs at 0.05 FDR threshold. For some genes, more than one eQTL was found using stepwise regression. In cases of multiple top SNPs with identical p-values (due to identical genotypes in the cohort) for an eQTL, one representative SNP among them was chosen at random. Paired-end RNA-Seq libraries for 53 rat eyes (one eye per rat) were aligned to the Rnor_6.0 genome using Spliced Transcripts Alignment to a Reference (STAR). The RNA-seq samples were tested for mismatches with their genotypes by inferring genotypes from RNA-seq reads and comparing them to DNA genotypes. We compared the RNA-inferred genotype from each rat to the DNA genotype of all other rats and found that 11 of the mismatched RNA samples were a strong match to a different DNA genotype, none of which already had a match, and could be recovered simply by relabeling the RNA samples, while the remaining two RNA samples had no high-similarity match in the DNA genotypes. Using these corrected RNA-seq/genotype pairs and removing the two remaining mismatches, we continued with 51 rat eye samples. The per-gene significance thresholds were computed by tensorQTL from data permutations, and false discovery rate (FDR) testing was performed across all genes using a q-value cutoff of 0.05. We also ran tensorQTL in cis nominal mode with larger cis-window sizes for genes of interest to obtain nominal p-values for all SNPs in the plotted regions. Log allelic fold change (aFC) of the eQTL used as a measure of effect size.
LABEL:
cis-eQTL related to IOP in HS outbred rats_log2FC
SCORE TYPE:
Effect
THRESHOLD:
<= 0.5
GENES IN THRESHOLD:
0
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DATE UPDATED:
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AUTHORS:
TITLE:
JOURNAL:
ABSTRACT:
Genes in threshold: 0
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