The aim of this study was to perform a GWAS in the heterogenous stock (HS) rat population to identify genomic regions that harbor variants responsible for the variation in intraocular pressure (IOP). We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to determine a genome-wide significance threshold. Both male and female HS rats (N=1,812) were used in the study. Genotyping-by-sequencing was used to obtain ~3.5M single nucleotide polymorphisms from each individual. We performed eQTL analysis using 51 rat eye samples. Log allelic fold change (aFC) of the eQTL used as a measure of effect size.
Authors:
Samuel Fowler, Tengfei Wang, Daniel Munro, Aman Kumar, Apurva S Chitre, T J Hollingsworth, Angel Garcia Martinez, Celine L St Pierre, Hannah Bimschleger, Jianjun Gao, Riyan Cheng, Pejman Mohammadi, Hao Chen, Abraham A Palmer, Oksana Polesskaya, Monica M JablonskiÂ
The aim of this study was to perform a GWAS in the heterogenous stock (HS) rat population to identify genomic regions that harbor variants responsible for the variation in intraocular pressure (IOP). We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to determine a genome-wide significance threshold. Both male and female HS rats (N=1,812) were used in the study. Genotyping-by-sequencing was used to obtain ~3.5M single nucleotide polymorphisms from each individual. We performed eQTL analysis using 51 rat eye samples. Log allelic fold change (aFC) of the eQTL used as a measure of effect size.
Authors:
Samuel Fowler, Tengfei Wang, Daniel Munro, Aman Kumar, Apurva S Chitre, T J Hollingsworth, Angel Garcia Martinez, Celine L St Pierre, Hannah Bimschleger, Jianjun Gao, Riyan Cheng, Pejman Mohammadi, Hao Chen, Abraham A Palmer, Oksana Polesskaya, Monica M JablonskiÂ
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.
Authors:
Samuel Fowler, Tengfei Wang, Daniel Munro, Aman Kumar, Apurva S Chitre, T J Hollingsworth, Angel Garcia Martinez, Celine L St Pierre, Hannah Bimschleger, Jianjun Gao, Riyan Cheng, Pejman Mohammadi, Hao Chen, Abraham A Palmer, Oksana Polesskaya, Monica M JablonskiÂ
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.
Authors:
Samuel Fowler, Tengfei Wang, Daniel Munro, Aman Kumar, Apurva S Chitre, T J Hollingsworth, Angel Garcia Martinez, Celine L St Pierre, Hannah Bimschleger, Jianjun Gao, Riyan Cheng, Pejman Mohammadi, Hao Chen, Abraham A Palmer, Oksana Polesskaya, Monica M JablonskiÂ
The aim of this study was to perform a GWAS in the heterogenous stock (HS) rat population to identify genomic regions that harbor variants responsible for the variation in intraocular pressure (IOP). We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to determine a genome-wide significance threshold. Both male and female HS rats (N=1,812) were used in the study. Genotyping-by-sequencing was used to obtain ~3.5M single nucleotide polymorphisms from each individual. We performed eQTL analysis using 51 rat eye samples. Log allelic fold change (aFC) of the eQTL used as a measure of effect size.
Authors:
Samuel Fowler, Tengfei Wang, Daniel Munro, Aman Kumar, Apurva S Chitre, T J Hollingsworth, Angel Garcia Martinez, Celine L St Pierre, Hannah Bimschleger, Jianjun Gao, Riyan Cheng, Pejman Mohammadi, Hao Chen, Abraham A Palmer, Oksana Polesskaya, Monica M JablonskiÂ
Striatum Gene Expression Correlates for AMDIST165 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The AMDIST165 measures Morphine distance (cm) travelled minutes 150-165 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for MORPH_NX measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The MORPH_NX measures Change in distance travelled last 15 min morphine-15 min naloxone under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for ACTI20_SAL measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The ACTI20_SAL measures Distance traveled (cm) during the fourth five minute bin after saline under the domain Ethanol. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for AMCNT135 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The AMCNT135 measures Morphine photocell counts minutes 120-135 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for AMCNT165 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The AMCNT165 measures Morphine photocell counts minutes 150-165 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for HAND_7HOURS measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The HAND_7HOURS measures Handling induced convulsions 7 hrs after ethanol under the domain Ethanol HIC. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT105 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT105 measures Morphine vertical activity counts minutes 90-105 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT105 measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT105 measures Morphine vertical activity counts minutes 90-105 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT120 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT120 measures Morphine vertical activity counts minutes 105-120 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT120 measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT120 measures Morphine vertical activity counts minutes 105-120 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT135 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT135 measures Morphine vertical activity counts minutes 120-135 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT135 measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT135 measures Morphine vertical activity counts minutes 120-135 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT165 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT165 measures Morphine vertical activity counts minutes 150-165 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Striatum Gene Expression Correlates for VERCNT165 measured in BXD RI Females obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The VERCNT165 measures Morphine vertical activity counts minutes 150-165 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Renthal W, Kumar A, Xiao G, Wilkinson M, Covington HE 3rd, Maze I, Sikder D, Robison AJ, LaPlant Q, Dietz DM, Russo SJ, Vialou V, Chakravarty S, Kodadek TJ, Stack A, Kabbaj M, Nestler EJ
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