About RatGTEx
Associated Studies
The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats (Preprint)
Other publications will be posted when available.
More info on the ratgenes.org eQTL page.
Tissues
The raw data for the tissues in this portal come from multiple studies. The processed data, however, may differ from the results reported in each study for a couple reasons:
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Different processing decisions could be made for each study, while the data in this portal are processed uniformly to facilitate comparison across tissues.
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The published study results are immutable, while new versions of data in this portal may be released, for example to improve quality or to use updated reference genome and annotations.
Nevertheless, we also host the original results from individual studies on the
Download page when available.
Tissue | Abbreviation | Samples | Originating study |
Infralimbic cortex | IL | 81 | P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration |
Lateral habenula | LHb | 81 | P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration |
Nucleus accumbens core | NAcc | 75 | P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration |
Orbitofrontal cortex | OFC | 80 | P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration |
Prelimbic cortex | PL | 80 | P50 DA037844 Y1-5, Project 2: Socially-acquired nicotine self-administration |
Eye | Eye | 51 | R01 EY021200: Genetic Modulators of Glaucoma |
Basolateral amygdala | BLA | 185 | U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model |
Nucleus accumbens core | NAcc2 | 188 | U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model |
Prelimbic cortex | PL2 | 191 | U01DA046077: Identification of Genetic Features of Delay Discounting Using a Heterogeneous Stock Rat Model |
Adipose | Adipose | 411 | R01DK106386: Systems genetics of adiposity traits in outbred rats |
Liver | Liver | 401 | R01DK106386: Systems genetics of adiposity traits in outbred rats |
Contact
For questions or comments related to the data or website, email Daniel Munro at dmunro@scripps.edu.
The RatGTEx data is currently available as a beta version. Please let us know if you'd like to use it for research so we can ensure everything is correct.
Acknowledgments
RatGTEx is produced by the NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844). It is not a project of the GTEx Consortium.
Code for visualizations was adapted from the GTEx
portal viz tools, and additional design considerations were inspired by the GTEx portal.
Data Specifications
The datasets provided in this portal conform to the following specifications to facilitate comparisons across tissues.
Processing
The ratgtex-pipeline repository contains all RNA-Seq and eQTL mapping pipeline code. The ratgtex-server-data repository contains code that processes those results into additional data files for download and for the API.
- Genome assembly: Rnor_6.0 (GCA_000001895.4)
- Annotations: Ensembl Rat
- RNA-Seq read counts, transformed as log2(count+1), were used to compute cis-eQTL effect sizes (allelic fold change).
- Inverse-quantile normalized expression values were used for eQTL mapping.
- eQTL mapping: tensorQTL. cis-eQTL mapping tested cis-windows +/- 1 Mb from each gene's transcription start site.
Formats
Gene expression ({tissue}.expr.{units}.bed.gz)
Expression tables are provided in BED format, with four columns describing the gene plus one column per sample. Only the transcription start sites are specified, not the whole gene length.
- #chr Chromosome name, e.g. '1'
- start Transcription start site. Coordinates in BED format are 0-based, so this is one less than the position as it is typically represented.
- end One higher than the start value. Thus, this would be the typical coordinate to represent the TSS.
- gene_id Ensembl gene ID
- {sample} Each additional column is labeled with the sample or rat ID and contains log2(count+1), TPM, or inverse-quantile normalized values.
All significant cis-eQTL gene-SNP pairs ({tissue}.cis_qtl_signif.txt.gz)
A compressed tab-separated table.
- gene_id Ensembl gene ID
- variant_id SNP ID (e.g. chr1:669562)
- tss_distance SNP position - TSS position, oriented on the gene's strand
- af Alternative allele frequency
- ma_samples Number of samples with minor allele
- ma_count Total number of minor alleles (i.e. no. het. + 2 * no. hom. alt.)
- pval_nominal Nominal p-value
- slope Coefficient for the SNP genotype in the linear model
- slope_se Standard error of the slope
- pval_nominal_threshold Gene-tissue-specific nominal p-value significance threshold as determined by permutations and transcriptome-wide FDR
Strong associations from trans-eQTL mapping ({tissue}.trans_qtl_pairs.txt.gz)
All measured SNPs genome-wide were tested against expression of each gene, and pairs with p-value < 1e-5 and > 5 Mb TSS distance are included here. Rows are sorted by variant location.
- variant_id SNP ID (e.g. chr1:669562)
- gene_id Ensembl gene ID
- pval Nominal p-value
- slope Coefficient (slope) for the SNP genotype in the linear model
- slope_se Standard error of the slope
- af Alternative allele frequency
Conditionally independent cis-eQTLs (eqtls_indep.txt)
A table of cis-eQTLs from all tissues. Stepwise regression was used to test for cis-eQTLs beyond and uncorrelated with the top cis-eQTL per gene.
- tissue Tissue abbreviation
- gene_id Ensembl gene ID
- gene_name Ensembl gene name
- num_var Number of cis-window variants tested for the specified gene in this tissue
- variant_id SNP ID (e.g. chr1:669562) for the top eQTL SNP (eSNP). In cases of tied top SNPs that are in 100% LD, one was randomly chosen among them.
- chrom Chromosome of the top SNP (e.g. "1")
- pos Position of the top SNP (bp)
- ref Reference allele for the top SNP
- alt Alternative allele for the top SNP
- af Alternative allele frequency
- tss_distance SNP position - TSS position, oriented on the gene's strand
- pval_nominal Nominal p-value
- slope Coefficient for the SNP genotype in the linear model
- slope_se Standard error of the slope
- pval_beta Empirical beta-approximated p-value
- rank The strongest cis-eQTL found per gene-tissue has rank 1, next-strongest has rank 2, etc.
- log2_aFC eQTL effect size measured as allelic fold change
Top association per gene (top_assoc.txt)
A table of the strongest variant-gene association per gene per tissue, even if not significant.
- tissue Tissue abbreviation
- gene_id Ensembl gene ID
- gene_name Ensembl gene name
- num_var Number of cis-window variants tested for the specified gene in this tissue
- variant_id SNP ID (e.g. chr1:669562) for the top eQTL SNP (eSNP). In cases of tied top SNPs that are in 100% LD, one was randomly chosen among them.
- chrom Chromosome of the top SNP (e.g. "1")
- pos Position of the top SNP (bp)
- ref Reference allele for the top SNP
- alt Alternative allele for the top SNP
- af Alternative allele frequency
- tss_distance SNP position - TSS position, oriented on the gene's strand
- pval_nominal Nominal p-value
- slope Coefficient for the SNP genotype in the linear model
- slope_se Standard error of the slope
- pval_beta Empirical beta-approximated p-value
- qval Q-value used to control transcriptome-wide FDR per tissue (q < 0.05 was used to determine significant cis-eQTLs)
- pval_nominal_threshold Gene-tissue-specific nominal p-value significance threshold as determined by permutations and transcriptome-wide FDR
- log2_aFC Effect size measured as allelic fold change