Effect of Human Genetic Variability on Gene Transcription in Dorsal Root Ganglia and Association with Pain Phenotypes
Marc Parisien1, Samar Khoury1, Anne-Julie Chabot-Doré1, Gary D. Slade2,3, Shad B. Smith2,4, Roger B. Fillingim5, Richard Ohrbach6, Joel D. Greenspan7, William Maixner2,4,8, Jeffrey S. Mogil1,9, Inna Belfer1,10, Luda Diatchenko1,10
- Supplementary Table 1
Pre-imputation statistics. The total number of SNPs is broken down into four classes: those which did not pass QC filetrs, those with high missing genotyping rate, those with low minor allelic counts and those which depart from the Hardy-Weinberg equilibrium.
- Supplementary Table 2
Post-imputation statistics. After imputation, total of ~82 million SNPs was detected (column B). After applying QC filters, there were 4.9 million SNPs left (column C). For comparison, post-imputation (column E) and pre-imputation (column F) SNP counts, corrected for linkage-disequilibrium, are compared to assess the gain (column G) in genotyping density following the imputation.
- Supplementary Table 3
Statistics for DRG eQTLs. The number of tests that were performed to detect gene-level cis-acting, gene-level trans-acting, exon-level cis-acting and exon-level trans-acting eQTLs in DRG. The threshold p-values calculated are shown at 5% and 1% FDR for cis-acting and trans-acting eQTLs, respectively
- Supplementary Table 4
Cis-acting, gene-level DRG eQTLs. FDR 5%.
- Supplementary Table 5
Cis-acting, exon-level DRG eQTLs. FDR 5%.
- Supplementary Table 6
Trans-acting, gene-level DRG eQTLs. FDR 1%.
- Supplementary Table 7
Trans-acting, exon-level DRG eQTLs. FDR 1%.
- Supplementary Table 8
eGenes in DRGs, blood and brain. eGenes for each tissue can be found in 1-way lists. eGenes lists shared by two (two 2-way) or common to all three (one 3-way) tissues are also included. Pathway Studio analyses for enrichment of GO term “biological process” are adjoined. Statistically significant P-values (Bonferroni threshold of 0.05 / number of rows) are highlighted in yellow.
- Supplementary Table 9
Master eGenes that are also DRG eGenes. The master eGenes list comes from a previous analysis of eQTLs in 53 tissues. Of these master eGenes, those also in DRGs are indicated.
- Supplementary Table 10
A list of DRG eQTLs were shown to be associated with diseases or related pathological phenotypes of interest using the NHGRI catalog. The lists also include DRG eQTLs, excluding eQTL from blood as well as excluding eQTLs from brain.
- Supplementary Table 11
Genes commonly implicated to pain pathways. The list is made from several sources: Algynomics’ Pain Panel V2, Cogenics’ Pain Research Panel, Pain Research Forum’s pain gene resource, and Amigo’s GO term 0019233. Accompanying forms show DRG eQTLs with the highest ranking of association with pain genes. The eQTLs are cis-acting, at the gene- and at the exon-level.
- Supplementary Table 12
Simultaneous DRG eQTL and OPPERA GWAS phenotype assessment score per SNP. The list shows SNPs that show strong association P-values with DRG mRNA amount at gene level as DRG eQTLs and show strong association P-vales in selected OPPERA GWAS phenotypes. TMD - Temporomandibular Disorders; LBP- Low Back Pain; PPT- pressure pain threshold; Mech- mechanical pain threshold; QSTthresh - QST heat pain threshold; QSTtoler - QST heat pain tolerance.
- DRG_matrix_eQTL.tar.gz (filesize: 866,552,124; md5sum: 2864c40ec03afdc83efbf9ba418e218e)
This UNIX tarball contains input files for matrix_eQTL in order to perform your own eQTL analyses in human dorsal root ganglions:
- genotype data
- phenotype data (gene- and exon-level probe intensities)
- positions of transcription start sites (TSS) for tested genes
- positions of exon boundaries for tested exons
- covariates informations (age, gender, 2 PCA, etc)
* all files are human-readable, but UNIX-formatted text files.
- Alan Edwards Centre for Research on Pain. McGill University, Montreal, Quebec, Canada.
- Center for Pain Research and Innovation, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University, Durham, NC, USA.
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, USA.
- Department of Oral Diagnostic Services, University at Buffalo, Buffalo, NY, USA.
- Department of Neural and Pain Sciences, and Brotman Facial Pain Clinic, University of Maryland Dental School, Baltimore, MD, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Psychology, McGill University, Montreal, Quebec, Canada.
- Correspondence should be addressed to: belferinna/at/gmail.com, luda.diatchenko/at/mcgill.ca