Developed by Ruofan Ding, Xudong Zou, Yangmei Qin, Gao Wang, Lei Li
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
xQTLbiolinks is a end-to-end bioinformatic tool for efficient mining and analyzing public and user-customized xQTLs data for the discovery of disease susceptibility genes. xQTLbiolinks consists of tailored functions that can be grouped into four modules: Data retrieval, Pre-processing, Analysis and Visualization.
Instructions, documentation, and tutorials can be found at here.
Quick Start
xQTLbiolinkscan be installed and used on any operator systems supporting R. The latest version (v1.6.3) is also available at GitHub repository and it can be installed throughdevtools::install_github("dingruofan/xQTLbiolinks”). For more details, please refer to the instructions at Installation section below.- Find the Query and download for xQTLs, gene, variant, tissue, sample and expressions.
- Find the Quick Start for a quick application of colocalization analysis with xQTLbiolinks. Go through a whole Case study of detection of casual vairants and genes in prostate cancer using
xQTLbiolinks. - The details and instructions of all functions implemented in xQTLbiolinks can be found here. Find more instructions with examples for visualizations here.
Citation
If you find the xQTLbiolinks package or any of the source code in this repository useful for your work, please cite:
Ruofan Ding, Xudong Zou, Yangmei Qin, Lihai Gong, Hui Chen, Xuelian Ma, Shouhong Guang, Chen Yu, Gao Wang, Lei Li, xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs, Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad440,
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
Dependencies
The xQTLbiolinks package has the following dependencies:
R packages: BiocGenerics, cowplot (>= 1.1.1), curl (>= 4.3.2), data.table (>= 1.14.2), DBI, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2 (>= 3.3.6), ggrepel, IRanges, jsonlite (>= 1.7.2), viridis, RMySQL, stringr (>= 1.4.0), utils (>= 4.0.3),VariantAnnotation, TxDb.Hsapiens.UCSC.hg38.knownGene, PupillometryR, coloc, hyprcoloc, knitr, rtracklayer, usethis, ggridges, CMplot, R.utils, ggforestplot.
Installation
To install this R package, you will need to have required package SummarizedExperiment installed from Bioconductor with following command:
if (!require("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
BiocManager::install("SummarizedExperiment") # For windows or linux
BiocManager::install("SummarizedExperiment",type="source") # For MACOnce you have installed the required package, you can then install xQTLbiolinks from CRAN or github(recommended) using following command:
# Install from github to get the latest version.
if(!require("devtools")){install.packages("devtools")}
devtools::install_github("dingruofan/xQTLbiolinks")1. xQTLbiolinks: query and download
RuoFan Daing
2023-05-03
Source: vignettes/query_download.Rmd
Load packages:
library(xQTLbiolinks)
library(data.table)
library(stringr)xQTL Query:
Query eQTLs:
Query significant eQTL associations with a variant id across all tissues:
eQTL_sig1 <- xQTLquery_eqtlSig("rs201327123")
eQTL_sig1 <- xQTLquery_eqtlSig("chr1_14677_G_A_b38")
# Query significant eQTL associations with a variant id in a specified tissue:
eQTL_sig1 <- xQTLquery_eqtlSig("chr1_14677_G_A_b38",
tissueSiteDetail="Skin - Sun Exposed (Lower leg)")eQTL_sig1#> variantId snpId gencodeId geneSymbol
#> 1: chr1_14677_G_A_b38 rs201327123 ENSG00000241860.6 RP11-34P13.13
#> 2: chr1_14677_G_A_b38 rs201327123 ENSG00000228463.9 AP006222.2
#> 3: chr1_14677_G_A_b38 rs201327123 ENSG00000228327.3 RP11-206L10.2
#> tissueSiteDetail pValue nes datasetId
#> 1: Skin - Sun Exposed (Lower leg) 8.00361e-11 0.857182 gtex_v8
#> 2: Skin - Sun Exposed (Lower leg) 3.30591e-09 -0.746043 gtex_v8
#> 3: Skin - Sun Exposed (Lower leg) 1.23187e-15 0.688242 gtex_v8Query eQTL associations for multiple variants:
varInfo <- xQTLquery_varPos(chrom="chr1", pos=c(1102708))
eQTL_sig2 <- xQTLquery_eqtlSig(variantName=varInfo$snpId)head(eQTL_sig2)#> variantId snpId gencodeId geneSymbol
#> 1: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 2: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 3: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 4: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 5: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 6: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> tissueSiteDetail pValue nes datasetId
#> 1: Brain - Amygdala 1.60336e-06 -0.459798 gtex_v8
#> 2: Brain - Anterior cingulate cortex (BA24) 8.66605e-07 -0.454671 gtex_v8
#> 3: Brain - Caudate (basal ganglia) 8.31578e-13 -0.472193 gtex_v8
#> 4: Brain - Cerebellar Hemisphere 2.37523e-06 -0.329395 gtex_v8
#> 5: Brain - Cerebellum 7.84906e-08 -0.392030 gtex_v8
#> 6: Brain - Cortex 9.13735e-13 -0.516023 gtex_v8Query eQTL associations by genes or tissues:
eQTL_sig3 <- xQTLquery_eqtlSig(genes="ATAD3B")
eQTL_sig3 <- xQTLquery_eqtlSig(genes=c("TP53", "SLC35E2B"), tissueSiteDetail= "Brain - Cerebellum")
eQTL_sig3 <- xQTLquery_eqtlSig(genes="ENSG00000141510.16")head(eQTL_sig3)#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7559785_G_A_b38 rs143094271 ENSG00000141510.16 TP53
#> 2: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 3: chr17_7675353_C_T_b38 rs35850753 ENSG00000141510.16 TP53
#> 4: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 5: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 6: chr17_7441178_C_T_b38 rs4151125 ENSG00000141510.16 TP53
#> tissueSiteDetail pValue nes datasetId
#> 1: Adipose - Subcutaneous 1.00467e-05 -0.403825 gtex_v8
#> 2: Adipose - Subcutaneous 8.68606e-10 -0.765786 gtex_v8
#> 3: Adipose - Subcutaneous 1.34916e-05 -0.401123 gtex_v8
#> 4: Cells - Cultured fibroblasts 9.07463e-06 -0.473760 gtex_v8
#> 5: Esophagus - Mucosa 5.18785e-07 -0.729226 gtex_v8
#> 6: Kidney - Cortex 7.27802e-07 -0.541302 gtex_v8Query eQTL associations with a variant-gene pair:
eQTL_sig4 <- xQTLquery_eqtlSig(variantName="rs1641513", genes="TP53")
eQTL_sig4 <- xQTLquery_eqtlSig(variantName="chr1_1667948_A_G_b38",
genes="SLC35E2B", tissueSiteDetail="Kidney - Cortex")eQTL_sig4#> variantId snpId gencodeId geneSymbol
#> 1: chr1_1667948_A_G_b38 rs368438548 ENSG00000189339.11 SLC35E2B
#> tissueSiteDetail pValue nes datasetId
#> 1: Kidney - Cortex 7.21369e-14 -1.05597 gtex_v8Multi-tissue eQTL metasoft results for a given gene and variant can be also queried using xQTLquery_eqtl, the results include: m-value (mValue), normalized effect size (nes), p-value (pValue) and standard error (se).
# Query with a gene symbol:
eqtlMeta <- xQTLquery_eqtl(gene="TP53")
# Query with a variant-gene pair:
eqtlMeta <- xQTLquery_eqtl(variantName="rs1641513",gene="TP53")head(eqtlMeta)#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 2: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 3: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 4: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 5: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 6: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> tissueSiteDetail pValue nes se mValue
#> 1: Adipose - Subcutaneous 0.00992404 0.1065590 0.0411719 0.988
#> 2: Adipose - Visceral (Omentum) 0.02456600 0.0985826 0.0436840 0.953
#> 3: Adrenal Gland 0.49990900 0.0580124 0.0858289 0.729
#> 4: Artery - Aorta 0.84236100 -0.0113147 0.0568473 0.670
#> 5: Artery - Coronary 0.51525500 0.0624194 0.0957326 0.745
#> 6: Artery - Tibial 0.01521470 0.1224370 0.0502740 0.963
#> datasetId
#> 1: gtex_v8
#> 2: gtex_v8
#> 3: gtex_v8
#> 4: gtex_v8
#> 5: gtex_v8
#> 6: gtex_v8Query sQTLs:
Query sQTL associations with rsid:
sQTL_sig1 <- xQTLquery_sqtlSig(variantName="rs201327123")
sQTL_sig1 <- xQTLquery_sqtlSig(variantName="chr1_14677_G_A_b38", tissueSiteDetail="Whole Blood")sQTL_sig1#> variantId snpId gencodeId geneSymbol
#> 1: chr1_14677_G_A_b38 rs201327123 ENSG00000227232.5 WASH7P
#> phenotypeId tissueSiteDetail pValue
#> 1: chr1:15947:16607:clu_40980:ENSG00000227232.5 Whole Blood 7.14888e-08
#> nes datasetId
#> 1: 0.756834 gtex_v8Query sQTL associations with gene symbol and gencode ID:
sQTL_sig2 <- xQTLquery_sqtlSig(genes="ENSG00000141510.16", tissueSiteDetail="Lung" )
sQTL_sig2 <- xQTLquery_sqtlSig(genes=c("ATAD3B", "MLH1"))sQTL_sig2#> variantId snpId gencodeId geneSymbol
#> 1: chr3_37136656_CAAAGA_C_b38 rs200076067 ENSG00000076242.14 MLH1
#> 2: chr3_37282912_C_T_b38 rs112128385 ENSG00000076242.14 MLH1
#> 3: chr1_1259424_T_C_b38 rs11804831 ENSG00000160072.19 ATAD3B
#> 4: chr1_1274256_A_G_b38 rs3737722 ENSG00000160072.19 ATAD3B
#> 5: chr1_1274972_A_G_b38 rs11260575 ENSG00000160072.19 ATAD3B
#> ---
#> 6330: chr1_1532105_T_C_b38 rs1987191 ENSG00000160072.19 ATAD3B
#> 6331: chr1_1533018_T_C_b38 rs6695186 ENSG00000160072.19 ATAD3B
#> 6332: chr1_1533095_G_A_b38 rs6677993 ENSG00000160072.19 ATAD3B
#> 6333: chr1_1533178_A_G_b38 rs6694773 ENSG00000160072.19 ATAD3B
#> 6334: chr1_1533253_C_T_b38 rs6690064 ENSG00000160072.19 ATAD3B
#> phenotypeId
#> 1: chr3:37040294:37047519:clu_44299:ENSG00000076242.14
#> 2: chr3:37040294:37047519:clu_44299:ENSG00000076242.14
#> 3: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> 4: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> 5: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> ---
#> 6330: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6331: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6332: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6333: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6334: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> tissueSiteDetail pValue nes datasetId
#> 1: Adipose - Subcutaneous 4.23971e-07 1.224370 gtex_v8
#> 2: Adipose - Subcutaneous 7.92886e-08 1.234820 gtex_v8
#> 3: Adipose - Subcutaneous 2.63274e-06 -0.334712 gtex_v8
#> 4: Adipose - Subcutaneous 1.92720e-06 -0.405750 gtex_v8
#> 5: Adipose - Subcutaneous 1.74607e-06 -0.389751 gtex_v8
#> ---
#> 6330: Whole Blood 3.35898e-07 -0.589917 gtex_v8
#> 6331: Whole Blood 4.09835e-06 -0.483704 gtex_v8
#> 6332: Whole Blood 2.61330e-07 -0.601543 gtex_v8
#> 6333: Whole Blood 5.63455e-07 -0.581156 gtex_v8
#> 6334: Whole Blood 3.35898e-07 -0.589917 gtex_v8Query sQTL associations with the variant-genes pair:
sQTL_sig3 <- xQTLquery_sqtlSig(variantName="rs201327123", genes=c("WASH7P","RP11-206L10.2"))
sQTL_sig3 <- xQTLquery_sqtlSig(variantName="chr17_7465085_A_G_b38", genes="TP53",
tissueSiteDetail="Lung")sQTL_sig3#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7465085_A_G_b38 rs546057177 ENSG00000141510.16 TP53
#> phenotypeId tissueSiteDetail
#> 1: chr17:7669690:7670609:clu_13833:ENSG00000141510.16 Lung
#> pValue nes datasetId
#> 1: 1.29439e-05 -0.566684 gtex_v8xQTLs Download
eQTL Download:
Download all eQTL associations for MLH1-rs13315355 pair in all tissues from all studies:
eqtlAssos <- xQTLdownload_eqtlAllAsso(gene="MLH1", variantName = "rs13315355", study="")Download all eQTL associations for gene ATP11B in Muscle - Skeletal from GTEx_V8:
eqtlAssos <- xQTLdownload_eqtlAllAsso("ATP11B", tissueLabel="Muscle - Skeletal")A more fast way to download eQTL association for a given gene is using “liLab” data source with paramater data_source="liLab" (only support GTEx tissues)
eqtlAssos <- xQTLdownload_eqtlAllAsso("ATP11B", tissueLabel="Muscle - Skeletal", data_source = "liLab")
# gencode ID is recommended:
eqtlAssos <- xQTLdownload_eqtlAllAsso("ENSG00000058063.15", tissueLabel="Muscle - Skeletal", data_source = "liLab")Download all eQTL associations for SNP rs11568818 in all tissues from all supported studies:
eqtlAssos <- xQTLdownload_eqtlAllAsso(variantName="rs11568818", study="")Download all eQTL associations of SNP rs11568818 in Muscle - Skeletal from GTEx_V8:
eqtlAssos <- xQTLdownload_eqtlAllAsso(variantName="chr11_102530930_T_C_b38",
tissueLabel="Muscle - Skeletal", study="GTEx_V8")Download all eQTL associations for gene ATP11B in CD4+ T cell from all supported studies:
eqtlAssos <- xQTLdownload_eqtlAllAsso(gene="MMP7",tissueLabel = "CD4+ T cell", study="")eqtlAssos#> variantId snpId type maf beta chrom
#> 1: chr11_101531348_T_C_b38 rs4254048 SNP 0.3097830 0.0909405 11
#> 2: chr11_101531533_A_G_b38 rs11224820 SNP 0.1548910 0.0891349 11
#> 3: chr11_101532218_A_G_b38 rs145907949 SNP 0.0135870 -0.5316370 11
#> 4: chr11_101532331_A_G_b38 rs138388841 SNP 0.0135870 0.1777300 11
#> 5: chr11_101532593_G_A_b38 rs61916052 SNP 0.0108696 0.1754850 11
#> ---
#> 19131: chr11_103529577_C_A_b38 rs12365191 SNP 0.0674157 0.4218230 11
#> 19132: chr11_103529693_T_TTGTG_b38 rs147237734 INDEL 0.3595510 0.1532910 11
#> 19133: chr11_103529825_T_C_b38 rs34949425 SNP 0.2247190 -0.1864580 11
#> 19134: chr11_103530122_T_C_b38 rs4754958 SNP 0.3089890 0.7059100 11
#> 19135: chr11_103530486_C_G_b38 rs17380432 SNP 0.3314610 -0.1633750 11
#> pos ref alt se median_tpm pValue totalAlleles
#> 1: 101531348 T C 0.210025 5.637 0.6655640 368
#> 2: 101531533 A G 0.256792 5.637 0.7289380 368
#> 3: 101532218 A G 0.837931 5.637 0.5266310 368
#> 4: 101532331 A G 0.807995 5.637 0.8261630 368
#> 5: 101532593 G A 1.179750 5.637 0.8819290 368
#> ---
#> 19131: 103529577 C A 0.438372 0.000 0.3390160 178
#> 19132: 103529693 T TTGTG 0.242597 0.000 0.5293910 178
#> 19133: 103529825 T C 0.273032 0.000 0.4967640 178
#> 19134: 103530122 T C 0.282450 0.000 0.0146332 178
#> 19135: 103530486 C G 0.246976 0.000 0.5103180 178
#> allelCounts imputationR2 condition molecular_trait_id
#> 1: 114 0.94063 None ENSG00000137673
#> 2: 57 0.95629 None ENSG00000137673
#> 3: 5 0.94880 None ENSG00000137673
#> 4: 6 0.69826 None ENSG00000137673
#> 5: 4 0.73096 None ENSG00000137673
#> ---
#> 19131: 12 0.97970 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19132: 63 0.87166 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19133: 40 0.98203 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19134: 55 0.98227 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19135: 59 0.98326 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> gene_id study_id tissue tissue_label
#> 1: ENSG00000137673 GENCORD CL_0000624 T cell
#> 2: ENSG00000137673 GENCORD CL_0000624 T cell
#> 3: ENSG00000137673 GENCORD CL_0000624 T cell
#> 4: ENSG00000137673 GENCORD CL_0000624 T cell
#> 5: ENSG00000137673 GENCORD CL_0000624 T cell
#> ---
#> 19131: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19132: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19133: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19134: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19135: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> qtl_group geneSymbol gencodeId_GTEX_v8
#> 1: T-cell MMP7 ENSG00000137673.8
#> 2: T-cell MMP7 ENSG00000137673.8
#> 3: T-cell MMP7 ENSG00000137673.8
#> 4: T-cell MMP7 ENSG00000137673.8
#> 5: T-cell MMP7 ENSG00000137673.8
#> ---
#> 19131: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19132: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19133: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19134: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19135: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8sQTL Download:
Download all sQTL associations for gene MMP7 and TP53 in Lung:
sqtlAssos<-xQTLdownload_sqtlAllAsso(genes=c("MMP7","TP53"), geneType = "geneSymbol", tissue="Lung")sqtlAssos#> rsid clu_name pValue beta se gencodeId
#> 1: rs4254048 clu_9701 0.4562150 0.05216700 0.0699585 ENSG00000137673.8
#> 2: rs11224820 clu_9701 0.0334606 -0.18979000 0.0889982 ENSG00000137673.8
#> 3: rs138388841 clu_9701 0.6221730 0.08717970 0.1768040 ENSG00000137673.8
#> 4: rs61916052 clu_9701 0.4701730 0.13079100 0.1809620 ENSG00000137673.8
#> 5: rs78752240 clu_9701 0.3274160 -0.33715300 0.3439250 ENSG00000137673.8
#> ---
#> 36276: rs59885278 clu_13833 0.2352270 0.22514800 0.1894450 ENSG00000141510.16
#> 36277: rs73251879 clu_13833 0.9783160 0.00368261 0.1354170 ENSG00000141510.16
#> 36278: rs58698225 clu_13833 0.9029850 0.00683635 0.0560565 ENSG00000141510.16
#> 36279: rs12935932 clu_13833 0.8615360 -0.01098430 0.0629434 ENSG00000141510.16
#> 36280: rs4346241 clu_13833 0.0140373 -0.16665600 0.0676048 ENSG00000141510.163’aQTL Download:
Download all 3’aQTL associations for gene MMP7 in Lung:
aqtlAssos <- xQTLdownload_xqtlAllAsso(genes=c("MMP7"), tissue="Lung")aqtlAssos#> rsid maf pValue beta se
#> 1: rs2701977 0.5743146 0.0007479838 -2.100113e-01 0.06186416
#> 2: rs1711402 0.8896104 0.0012343600 -3.024068e-01 0.09300488
#> 3: rs1784450 0.8896104 0.0014384863 -2.965600e-01 0.09248070
#> 4: rs948138 0.5512266 0.0015553106 -1.948009e-01 0.06118752
#> 5: chr11_102631148_C_T_b38 0.5808081 0.0017118558 -1.949774e-01 0.06179620
#> ---
#> 4178: rs2846715 0.5389611 0.9964685792 2.647676e-04 0.05978774
#> 4179: rs2846342 0.5389611 0.9964685792 2.647676e-04 0.05978774
#> 4180: rs4254048 0.3145743 0.9993855679 5.160473e-05 0.06697517
#> 4181: rs7123862 0.6360347 0.9996407735 2.974098e-05 0.06602145
#> 4182: rs10895249 0.3831169 0.9999300442 5.476405e-06 0.06242669
#> mRNA gencodeId
#> 1: NM_002423.5 ENSG00000137673.8
#> 2: NM_002423.5 ENSG00000137673.8
#> 3: NM_002423.5 ENSG00000137673.8
#> 4: NM_002423.5 ENSG00000137673.8
#> 5: NM_002423.5 ENSG00000137673.8
#> ---
#> 4178: NM_002423.5 ENSG00000137673.8
#> 4179: NM_002423.5 ENSG00000137673.8
#> 4180: NM_002423.5 ENSG00000137673.8
#> 4181: NM_002423.5 ENSG00000137673.8
#> 4182: NM_002423.5 ENSG00000137673.8mQTL Download:
Download all mQTL associations with cgp_id “cg00000221” in Prostate:
mQTL_meta<- xQTLdownload_mqtlmeta("Prostate")
mQTL_dt <- xQTLdownload_mQTL(cpg_id="cg00000221", tissue_name="Prostate")mQTL_dt#> variant_id gene maf pValue beta se
#> 1: chr17_48080661_G_A_b38 cg07625849 0.2238100 0.7905950 0.0295557 0.110913
#> 2: chr17_48080688_T_C_b38 cg07625849 0.2238100 0.0787432 0.2099310 0.117806
#> 3: chr17_48081171_T_C_b38 cg07625849 0.1380950 0.0706286 0.2153530 0.117448
#> 4: chr17_48081344_A_T_b38 cg07625849 0.0190476 0.6815340 -0.1598080 0.387928
#> 5: chr17_48081546_C_G_b38 cg07625849 0.2238100 0.0787432 0.2099310 0.117806
#> ---
#> 2774: chr17_49079069_C_G_b38 cg07625849 0.2238100 0.3348770 -0.1138980 0.117360
#> 2775: chr17_49079242_G_A_b38 cg07625849 0.0952381 0.1356170 0.2237770 0.148361
#> 2776: chr17_49079593_G_A_b38 cg07625849 0.0380952 0.3482250 -0.2615080 0.277058
#> 2777: chr17_49079687_A_T_b38 cg07625849 0.0142857 0.4095380 0.3410300 0.411232
#> 2778: chr17_49080066_G_A_b38 cg07625849 0.1809520 0.1526370 -0.1839900 0.127350hQTL Download:
Download all hQTL associations for H3K4ME1 in T cell:
hqtlmeta <- xQTLdownload_hqtlmeta(histone_type="H3K4ME1", cell_type="T cell")
hQTL_dt <- xQTLdownload_hqtl(phenotype_id="10:10458128-10465096",
histone_type="H3K4ME1", cell_type="T cell")hQTL_dt#> rsid gene maf pValue beta se
#> 1: rs950228 10:10458128:10465096 0.4850 0.3871 -0.12300 0.1422
#> 2: rs12783041 10:10458128:10465096 0.3850 0.4063 0.11590 0.1396
#> 3: rs7903944 10:10458128:10465096 0.4825 0.4623 -0.10580 0.1439
#> 4: rs10905556 10:10458128:10465096 0.4800 0.3548 -0.13040 0.1409
#> 5: rs34488055 10:10458128:10465096 0.1275 0.7625 -0.06456 0.2136
#> ---
#> 4209: rs72777637 10:10458128:10465096 0.0550 0.8334 0.06993 0.3325
#> 4210: rs2440112 10:10458128:10465096 0.7375 0.5641 -0.10610 0.1840
#> 4211: rs77085282 10:10458128:10465096 0.0525 0.5223 0.20470 0.3199
#> 4212: rs7068574 10:10458128:10465096 0.1900 0.8650 -0.03029 0.1782
#> 4213: rs2499927 10:10458128:10465096 0.0525 0.2223 0.42320 0.3468
#> variantId
#> 1: 10:9458147_A_G
#> 2: 10:9459295_T_C
#> 3: 10:9459626_C_T
#> 4: 10:9460058_C_T
#> 5: 10:9463102_A_G
#> ---
#> 4209: 10:11461313_T_C
#> 4210: 10:11462143_T_C
#> 4211: 10:11464056_T_C
#> 4212: 10:11464106_G_C
#> 4213: 10:11464602_T_ASingle-cell eQTLs (sc-eQTLs) Download:
Download Cell-type eQTLs for gene TP53 in B cell from study Resztak2022biorxiv:
# Get details of sc-eQTL study:
study_info <- xQTLquery_scInfo()
sceQTL_dt <- xQTLdownload_sc(gene="TP53", cell_type = "B Cell", cell_state="-",
qtl_type="Cell-type-specific eQTL", study_name = "Resztak2022biorxiv")sceQTL_dt#> beta cellType chromosome geneSymbol pValue pos
#> 1: -0.0120341 B Cell chr17 TP53 0.894893 7639177
#> 2: -0.0122527 B Cell chr17 TP53 0.892879 7639273
#> 3: -0.0866685 B Cell chr17 TP53 0.340513 7639553
#> 4: -0.0135121 B Cell chr17 TP53 0.881551 7639699
#> 5: -0.0181303 B Cell chr17 TP53 0.839595 7640154
#> ---
#> 260: -0.162146 B Cell chr17 TP53 0.0816707 7697870
#> 261: 0.13485 B Cell chr17 TP53 0.235491 7719119
#> 262: -0.121788 B Cell chr17 TP53 0.303225 7722187
#> 263: 0.070017 B Cell chr17 TP53 0.602875 7722656
#> 264: 0.18766 B Cell chr17 TP53 0.0818137 7724742
#> qtlType se snpId
#> 1: Cell-type-specific eQTL 0.0910877781405 rs2430948
#> 2: Cell-type-specific eQTL 0.0909884473621 rs1642795
#> 3: Cell-type-specific eQTL 0.0909282976755 rs1642796
#> 4: Cell-type-specific eQTL 0.0906832041021 rs1642797
#> 5: Cell-type-specific eQTL 0.0895714697899 rs12450254
#> ---
#> 260: Cell-type-specific eQTL 0.0931299007474 rs1393370347
#> 261: Cell-type-specific eQTL 0.113669645877 rs373872446
#> 262: Cell-type-specific eQTL 0.11829336382 rs1052202011
#> 263: Cell-type-specific eQTL 0.134578050437 rs8070743
#> 264: Cell-type-specific eQTL 0.107834576496 rs370880934
#> study variantId
#> 1: Resztak2022biorxiv_qtl rs2430948
#> 2: Resztak2022biorxiv_qtl rs1642795
#> 3: Resztak2022biorxiv_qtl rs1642796
#> 4: Resztak2022biorxiv_qtl rs1642797
#> 5: Resztak2022biorxiv_qtl rs12450254
#> ---
#> 260: Resztak2022biorxiv_qtl rs1393370347
#> 261: Resztak2022biorxiv_qtl rs373872446
#> 262: Resztak2022biorxiv_qtl rs1052202011
#> 263: Resztak2022biorxiv_qtl rs8070743
#> 264: Resztak2022biorxiv_qtl rs370880934Query details of gene, variant, tissue and samples in GTEx:
Query gene details with gene symbols, versioned or unversioned gencode ID:
geneInfo <- xQTLquery_gene("TP53")
geneInfo <- xQTLquery_gene(c("tp53","naDK","SDF4") )
geneInfo <- xQTLquery_gene(c("ENSG00000210195.2","ENSG00000078808"))geneInfo#> genes genesUpper geneSymbol gencodeId
#> 1: ENSG00000210195.2 ENSG00000210195.2 MT-TT ENSG00000210195.2
#> 2: ENSG00000078808 ENSG00000078808 SDF4 ENSG00000078808.16
#> entrezGeneId geneType chromosome start end strand tss
#> 1: NA Mt tRNA chrM 15888 15953 + 15888
#> 2: 51150 protein coding chr1 1216908 1232031 - 1232031
#> gencodeVersion genomeBuild
#> 1: v26 GRCh38/hg38
#> 2: v26 GRCh38/hg38
#> description
#> 1: mitochondrially encoded tRNA threonine [Source:HGNC Symbol;Acc:HGNC:7499]
#> 2: stromal cell derived factor 4 [Source:HGNC Symbol;Acc:HGNC:24188]Query variants using dbSNP ID or variant ID:
varInfo <- xQTLquery_varId("rs12596338")
varInfo <- xQTLquery_varId("chr11_66561248_T_C_b38")
varInfo <- xQTLquery_varPos(chrom="chr1", pos=c(1102708,1105739))varInfo#> variantId snpId b37VariantId chromosome pos ref alt
#> 1: chr1_1102708_G_C_b38 rs66622470 1_1038088_G_C_b37 chr1 1102708 G C
#> datasetId maf01 shorthand
#> 1: gtex_v8 TRUE NAQuery tissue using tissue name:
tissueAll <- xQTLquery_tissue() # fetch all tissues in GTEx
Brain <- xQTLquery_tissue("Brain")Brain#> colorHex colorRgb datasetId eGeneCount eqtlAgeMaxFemale eqtlAgeMaxMale
#> 1: EEEE00 238,238,0 gtex_v8 3726 70 70
#> 2: EEEE00 238,238,0 gtex_v8 5640 70 70
#> 3: EEEE00 238,238,0 gtex_v8 8362 70 70
#> 4: EEEE00 238,238,0 gtex_v8 10027 70 70
#> 5: EEEE00 238,238,0 gtex_v8 11240 70 70
#> 6: EEEE00 238,238,0 gtex_v8 9082 70 70
#> 7: EEEE00 238,238,0 gtex_v8 7335 70 70
#> 8: EEEE00 238,238,0 gtex_v8 5517 70 70
#> 9: EEEE00 238,238,0 gtex_v8 5499 70 70
#> 10: EEEE00 238,238,0 gtex_v8 8198 70 70
#> 11: EEEE00 238,238,0 gtex_v8 6902 70 70
#> 12: EEEE00 238,238,0 gtex_v8 4483 70 70
#> 13: EEEE00 238,238,0 gtex_v8 3301 70 70
#> eqtlAgeMeanFemale eqtlAgeMeanMale eqtlAgeMinFemale eqtlAgeMinMale
#> 1: 57.6 58.2 28 20
#> 2: 57.2 58.2 24 20
#> 3: 56.8 58.5 24 22
#> 4: 57.5 57.5 24 20
#> 5: 58.7 56.7 24 20
#> 6: 58.2 57.3 24 20
#> 7: 59.1 58.6 28 20
#> 8: 58.9 58.2 28 20
#> 9: 59.6 58.7 28 20
#> 10: 57.7 58.2 24 20
#> 11: 58.4 58.1 28 20
#> 12: 58.2 58.4 28 22
#> 13: 56.2 58.6 24 20
#> eqtlSampleCountFemale eqtlSampleCountMale expressedGeneCount hasEGenes
#> 1: 37 92 28196 TRUE
#> 2: 42 105 28921 TRUE
#> 3: 52 142 29230 TRUE
#> 4: 51 124 29538 TRUE
#> 5: 58 151 30106 TRUE
#> 6: 64 141 29560 TRUE
#> 7: 48 127 29132 TRUE
#> 8: 49 116 28625 TRUE
#> 9: 47 123 29502 TRUE
#> 10: 55 147 29339 TRUE
#> 11: 42 128 28335 TRUE
#> 12: 48 78 28352 TRUE
#> 13: 33 81 28050 TRUE
#> hasSGenes mappedInHubmap rnaSeqAgeMaxFemale rnaSeqAgeMaxMale
#> 1: TRUE FALSE 70 70
#> 2: TRUE FALSE 70 70
#> 3: TRUE FALSE 70 70
#> 4: TRUE FALSE 70 70
#> 5: TRUE FALSE 70 70
#> 6: TRUE FALSE 70 70
#> 7: TRUE FALSE 70 70
#> 8: TRUE FALSE 70 70
#> 9: TRUE FALSE 70 70
#> 10: TRUE FALSE 70 70
#> 11: TRUE FALSE 70 70
#> 12: TRUE FALSE 70 70
#> 13: TRUE FALSE 70 70
#> rnaSeqAgeMeanFemale rnaSeqAgeMeanMale rnaSeqAgeMinFemale rnaSeqAgeMinMale
#> 1: 57.2 58.9 28 20
#> 2: 57.2 58.8 24 20
#> 3: 56.9 59.2 24 22
#> 4: 57.3 58.5 24 20
#> 5: 58.3 57.3 24 20
#> 6: 57.8 58.2 24 20
#> 7: 58.7 59.1 28 20
#> 8: 58.3 58.8 28 20
#> 9: 59.3 59.0 28 20
#> 10: 57.7 58.8 24 20
#> 11: 58.4 58.5 28 20
#> 12: 58.1 59.7 28 22
#> 13: 56.2 59.3 24 20
#> rnaSeqAndGenotypeSampleCount rnaSeqSampleCount rnaSeqSampleCountFemale
#> 1: 129 152 45
#> 2: 147 176 48
#> 3: 194 246 63
#> 4: 175 215 58
#> 5: 209 241 67
#> 6: 205 255 74
#> 7: 175 209 56
#> 8: 165 197 54
#> 9: 170 202 55
#> 10: 202 246 64
#> 11: 170 205 49
#> 12: 126 159 57
#> 13: 114 139 38
#> rnaSeqSampleCountMale sGeneCount
#> 1: 107 892
#> 2: 128 1238
#> 3: 183 1809
#> 4: 157 2397
#> 5: 174 2786
#> 6: 181 2048
#> 7: 153 1684
#> 8: 143 1185
#> 9: 147 1414
#> 10: 182 1881
#> 11: 156 1350
#> 12: 102 1144
#> 13: 101 814
#> samplingSite
#> 1: Amygdala (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 2: Anterior cingulate cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 3: Caudate (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 4: Cerebellar hemisphere (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 5: Right cerebellum (sampled at donor collection site and preserved in PAXgene fixative).
#> 6: Right cerebral frontal pole cortex (sampled at donor collection site and preserved in PAXgene fixative).
#> 7: Right cerebral frontal pole cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 8: Hippocampus (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 9: Hypothalamus (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 10: Nucleus accumbens basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 11: Putamen basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 12: Spinal cord (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 13: Substantia nigra (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> tissueSite tissueSiteDetail tissueSiteDetailAbbr
#> 1: Brain Brain - Amygdala BRNAMY
#> 2: Brain Brain - Anterior cingulate cortex (BA24) BRNACC
#> 3: Brain Brain - Caudate (basal ganglia) BRNCDT
#> 4: Brain Brain - Cerebellar Hemisphere BRNCHB
#> 5: Brain Brain - Cerebellum BRNCHA
#> 6: Brain Brain - Cortex BRNCTXA
#> 7: Brain Brain - Frontal Cortex (BA9) BRNCTXB
#> 8: Brain Brain - Hippocampus BRNHPP
#> 9: Brain Brain - Hypothalamus BRNHPT
#> 10: Brain Brain - Nucleus accumbens (basal ganglia) BRNNCC
#> 11: Brain Brain - Putamen (basal ganglia) BRNPTM
#> 12: Brain Brain - Spinal cord (cervical c-1) BRNSPC
#> 13: Brain Brain - Substantia nigra BRNSNG
#> tissueSiteDetailId uberonId
#> 1: Brain_Amygdala 0001876
#> 2: Brain_Anterior_cingulate_cortex_BA24 0009835
#> 3: Brain_Caudate_basal_ganglia 0001873
#> 4: Brain_Cerebellar_Hemisphere 0002037
#> 5: Brain_Cerebellum 0002037
#> 6: Brain_Cortex 0001870
#> 7: Brain_Frontal_Cortex_BA9 0009834
#> 8: Brain_Hippocampus 0001954
#> 9: Brain_Hypothalamus 0001898
#> 10: Brain_Nucleus_accumbens_basal_ganglia 0001882
#> 11: Brain_Putamen_basal_ganglia 0001874
#> 12: Brain_Spinal_cord_cervical_c-1 0006469
#> 13: Brain_Substantia_nigra 0002038Query sample using tissue name or sample ID:
sampleInfo <- xQTLquery_sampleByTissue("Brain - Amygdala" )
sampleInfo <- xQTLquery_sampleByTissue(tissueSiteDetail="Liver", pathologyNotesCategories=TRUE)
sampleIds <- c("GTEX-11NUK-0011-R4a-SM-DO12B", "GTEX-11ONC-0011-R4b-SM-DO93H",
"GTEX-11DXY-0526-SM-5EGGQ", "GTEX-13OVJ-1026-SM-5IFGI")
sampleInfo <- xQTLquery_sampleBySampleId(sampleIds)sampleInfo#> ageBracket aliquotId autolysisScore dataType datasetId
#> 1: 60-69 SM-5EGGQ Mild RNASEQ gtex_v8
#> 2: 50-59 SM-DO12B <NA> RNASEQ gtex_v8
#> 3: 60-69 SM-DO93H <NA> RNASEQ gtex_v8
#> 4: 50-59 SM-5IFGI Mild EXCLUDE gtex_v8
#> hardyScale ischemicTime ischemicTimeGroup
#> 1: Fast death - natural causes 891 601 - 900
#> 2: Fast death - natural causes 864 601 - 900
#> 3: Fast death - natural causes 587 301 - 600
#> 4: Fast death - natural causes 1129 901 - 1200
#> pathologyNotes rin
#> 1: 2 pieces, congestion 6.8
#> 2: <NA> 7.1
#> 3: <NA> 7.1
#> 4: 2 pieces; cirrhosis, steatosis, Mallory hyaline c/w alcoholic cirrhosis 6.2
#> sampleId sex subjectId tissueSampleId
#> 1: GTEX-11DXY-0526-SM-5EGGQ male GTEX-11DXY GTEX-11DXY-0526
#> 2: GTEX-11NUK-0011-R4a-SM-DO12B male GTEX-11NUK GTEX-11NUK-0011-R4a
#> 3: GTEX-11ONC-0011-R4b-SM-DO93H male GTEX-11ONC GTEX-11ONC-0011-R4b
#> 4: GTEX-13OVJ-1026-SM-5IFGI female GTEX-13OVJ GTEX-13OVJ-1026
#> tissueSiteDetail tissueSiteDetailId uberonId
#> 1: Liver Liver 0001114
#> 2: Brain - Amygdala Brain_Amygdala 0001876
#> 3: Brain - Amygdala Brain_Amygdala 0001876
#> 4: Liver Liver 0001114xQTL expression download
Download normalized expression of gene for a eQTL pair.
Download exp with variant-gene pair in different tissues:
eQTLexp <- xQTLdownload_eqtlExp(variantName="rs1641513",gene="TP53", tissueSiteDetail="Liver")Download expression using variant ID and gencode ID:
eQTLexp <- xQTLdownload_eqtlExp(variantName="chr1_14677_G_A_b38",gene="ENSG00000228463.9",
tissueSiteDetail="Stomach")eQTLexp#> normExp genotypes
#> 1: -2.1600444 0
#> 2: 0.1509692 0
#> 3: 0.7464682 0
#> 4: -0.2613195 0
#> 5: 0.9212440 0
#> ---
#> 320: 0.9944579 0
#> 321: -0.9450852 0
#> 322: -0.7566981 0
#> 323: 1.3266775 0
#> 324: 0.8750651 0Download normalized intron-excision ratio of intron for a sQTL pair.
Download normalized intron-excision ratio in different tissues:
sQTLratio <- xQTLdownload_sqtlExp(variantName="rs1450891501",
phenotypeId="chr1:497299:498399:clu_54863:ENSG00000239906.1",
tissueSiteDetail="Lung")Dowload normalized intron-excision ratio using variant ID:
sQTLratio <- xQTLdownload_sqtlExp(variantName="chr1_1259424_T_C_b38",
phenotypeId=" chr1:1487914:1489204:clu_52051:ENSG00000160072.19",
tissueSiteDetail="Adipose - Subcutaneous")sQTLratio#> normExp genotypes
#> 1: 1.39907974 0
#> 2: -0.02638638 0
#> 3: 1.43450451 1
#> 4: 0.25182051 0
#> 5: -1.94683842 2
#> ---
#> 577: 1.82050424 2
#> 578: 1.24869651 1
#> 579: 0.61319702 0
#> 580: -2.59815685 1
#> 581: -1.69950516 1eGene/sGene download
Download details of eGenes (eQTL Genes) for a specified gene or a tissue.
eGeneInfo <- xQTLdownload_egene(tissueSiteDetail="Prostate", recordPerChunk=2000)
eGeneInfo <- xQTLdownload_egene("TP53")eGeneInfo#> gencodeId geneSymbol entrezGeneId geneType chromosome start
#> 1: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 2: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 3: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 4: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 5: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 6: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 7: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> end tss log2AllelicFoldChange empiricalPValue pValue
#> 1: 7687550 7687550 -0.680804 4.94757e-06 8.68606e-10
#> 2: 7687550 7687550 -0.500061 2.63392e-02 9.07463e-06
#> 3: 7687550 7687550 -0.501278 2.00743e-03 5.18785e-07
#> 4: 7687550 7687550 -0.359329 1.43349e-03 6.52895e-07
#> 5: 7687550 7687550 -1.243570 1.55063e-03 5.70716e-07
#> 6: 7687550 7687550 -0.541348 1.38551e-06 2.05198e-10
#> 7: 7687550 7687550 -0.550911 2.00129e-07 3.00426e-11
#> pValueThreshold qValue tissueSiteDetail datasetId
#> 1: 1.26507e-04 3.94849e-06 Adipose - Subcutaneous gtex_v8
#> 2: 1.52146e-04 1.03629e-02 Cells - Cultured fibroblasts gtex_v8
#> 3: 1.13047e-04 1.25547e-03 Esophagus - Mucosa gtex_v8
#> 4: 5.80918e-06 2.32936e-02 Kidney - Cortex gtex_v8
#> 5: 3.88929e-05 2.94618e-03 Pituitary gtex_v8
#> 6: 1.18255e-04 1.28231e-06 Skin - Not Sun Exposed (Suprapubic) gtex_v8
#> 7: 1.60112e-04 1.50952e-07 Skin - Sun Exposed (Lower leg) gtex_v8Download details of sGenes (sQTL Genes) for a specified gene or a tissue.
sGeneInfo <- xQTLdownload_sgene(tissueSiteDetail="Liver")
sGeneInfo <- xQTLdownload_sgene(gene="DDX11", tissueSiteDetail="Liver" )eGeneInfo#> gencodeId geneSymbol entrezGeneId geneType chromosome start
#> 1: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 2: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 3: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 4: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 5: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 6: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 7: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> end tss log2AllelicFoldChange empiricalPValue pValue
#> 1: 7687550 7687550 -0.680804 4.94757e-06 8.68606e-10
#> 2: 7687550 7687550 -0.500061 2.63392e-02 9.07463e-06
#> 3: 7687550 7687550 -0.501278 2.00743e-03 5.18785e-07
#> 4: 7687550 7687550 -0.359329 1.43349e-03 6.52895e-07
#> 5: 7687550 7687550 -1.243570 1.55063e-03 5.70716e-07
#> 6: 7687550 7687550 -0.541348 1.38551e-06 2.05198e-10
#> 7: 7687550 7687550 -0.550911 2.00129e-07 3.00426e-11
#> pValueThreshold qValue tissueSiteDetail datasetId
#> 1: 1.26507e-04 3.94849e-06 Adipose - Subcutaneous gtex_v8
#> 2: 1.52146e-04 1.03629e-02 Cells - Cultured fibroblasts gtex_v8
#> 3: 1.13047e-04 1.25547e-03 Esophagus - Mucosa gtex_v8
#> 4: 5.80918e-06 2.32936e-02 Kidney - Cortex gtex_v8
#> 5: 3.88929e-05 2.94618e-03 Pituitary gtex_v8
#> 6: 1.18255e-04 1.28231e-06 Skin - Not Sun Exposed (Suprapubic) gtex_v8
#> 7: 1.60112e-04 1.50952e-07 Skin - Sun Exposed (Lower leg) gtex_v8Gene expression download
Download normalized gene expression at the sample level in a specified tissue:
Download gene expression with a genecode ID:
expProfiles <- xQTLdownload_exp("ENSG00000210195.2", tissueSiteDetail="Liver")Download gene expression into a SummarizedExperiment object:
expProfiles <- xQTLdownload_exp("ENSG00000210195.2", tissueSiteDetail="Liver",
toSummarizedExperiment=TRUE)
# extract expression profile from SummarizedExperiment object:
expDT <- SummarizedExperiment::assay(expProfiles)
# extract samples' detail from SummarizedExperiment object:
sampleDT <- SummarizedExperiment::colData(expProfiles)Download gene expression profiles for multiple genes:
expProfiles <- xQTLdownload_exp(c("tp53","naDK","SDF4"),
tissueSiteDetail="Artery - Coronary",
pathologyNotesCategories=TRUE)Download using versioned and unversioned gencode Id.
expProfiles <- xQTLdownload_exp(c("ENSG00000141510.16","ENSG00000008130.15","ENSG00000078808"),
tissueSiteDetail="Artery - Coronary")expProfiles[,1:12]#> gencodeId genes geneSymbol datasetId tissueSiteDetailId
#> 1 ENSG00000141510.16 ENSG00000141510.16 TP53 gtex_v8 Artery_Coronary
#> 2 ENSG00000008130.15 ENSG00000008130.15 NADK gtex_v8 Artery_Coronary
#> 3 ENSG00000078808.16 ENSG00000078808 SDF4 gtex_v8 Artery_Coronary
#> unit genesUpper GTEX-1117F-0626-SM-5N9CS GTEX-1122O-0426-SM-5H12G
#> 1 TPM ENSG00000141510.16 27.83 16.88
#> 2 TPM ENSG00000008130.15 77.78 60.54
#> 3 TPM ENSG00000078808.16 210.60 205.60
#> GTEX-117YX-1726-SM-5GZZS GTEX-11DXX-0826-SM-5GZZP GTEX-11DXY-1126-SM-5987W
#> 1 20.25 24.36 20.53
#> 2 69.14 62.15 31.90
#> 3 203.60 184.10 188.60Download median expression of all samples for specified genes across tissues.
geneMedExp <- xQTLdownload_geneMedExp(genes=c("TP53", "IRF5"))geneMedExp#> gencodeId geneSymbol median tissueSiteDetail
#> 1: ENSG00000128604.19 IRF5 8.53482 Adipose - Subcutaneous
#> 2: ENSG00000128604.19 IRF5 6.12789 Adipose - Visceral (Omentum)
#> 3: ENSG00000128604.19 IRF5 4.67700 Adrenal Gland
#> 4: ENSG00000128604.19 IRF5 5.29194 Artery - Aorta
#> 5: ENSG00000128604.19 IRF5 6.60034 Artery - Coronary
#> ---
#> 104: ENSG00000141510.16 TP53 14.82610 Testis
#> 105: ENSG00000141510.16 TP53 19.66310 Thyroid
#> 106: ENSG00000141510.16 TP53 29.49970 Uterus
#> 107: ENSG00000141510.16 TP53 25.29200 Vagina
#> 108: ENSG00000141510.16 TP53 7.69810 Whole Blood
#> entrezGeneId geneType chromosome start end strand
#> 1: 3663 protein coding chr7 128937612 128950035 +
#> 2: 3663 protein coding chr7 128937612 128950035 +
#> 3: 3663 protein coding chr7 128937612 128950035 +
#> 4: 3663 protein coding chr7 128937612 128950035 +
#> 5: 3663 protein coding chr7 128937612 128950035 +
#> ---
#> 104: 7157 protein coding chr17 7661779 7687550 -
#> 105: 7157 protein coding chr17 7661779 7687550 -
#> 106: 7157 protein coding chr17 7661779 7687550 -
#> 107: 7157 protein coding chr17 7661779 7687550 -
#> 108: 7157 protein coding chr17 7661779 7687550 -
#> tss
#> 1: 128937612
#> 2: 128937612
#> 3: 128937612
#> 4: 128937612
#> 5: 128937612
#> ---
#> 104: 7687550
#> 105: 7687550
#> 106: 7687550
#> 107: 7687550
#> 108: 76875501. xQTLbiolinks: query and download
1. xQTLbiolinks：查询和下载
RuoFan Daing 若凡戴
2023-05-03
Source: vignettes/query_download.Rmd资料来源：vignettes/query_download。Rmd
Load packages: 加载包：
library(xQTLbiolinks)
library(data.table)
library(stringr)xQTL Query: xQTL 查询：
Query eQTLs: 查询 eQTL：
Query significant eQTL associations with a variant id across all tissues:
查询所有组织中具有变异 id 的显著 eQTL 关联：
eQTL_sig1 <- xQTLquery_eqtlSig("rs201327123")
eQTL_sig1 <- xQTLquery_eqtlSig("chr1_14677_G_A_b38")
# Query significant eQTL associations with a variant id in a specified tissue:
eQTL_sig1 <- xQTLquery_eqtlSig("chr1_14677_G_A_b38",
tissueSiteDetail="Skin - Sun Exposed (Lower leg)")eQTL_sig1#> variantId snpId gencodeId geneSymbol
#> 1: chr1_14677_G_A_b38 rs201327123 ENSG00000241860.6 RP11-34P13.13
#> 2: chr1_14677_G_A_b38 rs201327123 ENSG00000228463.9 AP006222.2
#> 3: chr1_14677_G_A_b38 rs201327123 ENSG00000228327.3 RP11-206L10.2
#> tissueSiteDetail pValue nes datasetId
#> 1: Skin - Sun Exposed (Lower leg) 8.00361e-11 0.857182 gtex_v8
#> 2: Skin - Sun Exposed (Lower leg) 3.30591e-09 -0.746043 gtex_v8
#> 3: Skin - Sun Exposed (Lower leg) 1.23187e-15 0.688242 gtex_v8Query eQTL associations for multiple variants:
查询多个变体的 eQTL 关联：
varInfo <- xQTLquery_varPos(chrom="chr1", pos=c(1102708))
eQTL_sig2 <- xQTLquery_eqtlSig(variantName=varInfo$snpId)head(eQTL_sig2)#> variantId snpId gencodeId geneSymbol
#> 1: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 2: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 3: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 4: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 5: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 6: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> tissueSiteDetail pValue nes datasetId
#> 1: Brain - Amygdala 1.60336e-06 -0.459798 gtex_v8
#> 2: Brain - Anterior cingulate cortex (BA24) 8.66605e-07 -0.454671 gtex_v8
#> 3: Brain - Caudate (basal ganglia) 8.31578e-13 -0.472193 gtex_v8
#> 4: Brain - Cerebellar Hemisphere 2.37523e-06 -0.329395 gtex_v8
#> 5: Brain - Cerebellum 7.84906e-08 -0.392030 gtex_v8
#> 6: Brain - Cortex 9.13735e-13 -0.516023 gtex_v8Query eQTL associations by genes or tissues:
通过基因或组织查询 eQTL 关联：
eQTL_sig3 <- xQTLquery_eqtlSig(genes="ATAD3B")
eQTL_sig3 <- xQTLquery_eqtlSig(genes=c("TP53", "SLC35E2B"), tissueSiteDetail= "Brain - Cerebellum")
eQTL_sig3 <- xQTLquery_eqtlSig(genes="ENSG00000141510.16")head(eQTL_sig3)#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7559785_G_A_b38 rs143094271 ENSG00000141510.16 TP53
#> 2: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 3: chr17_7675353_C_T_b38 rs35850753 ENSG00000141510.16 TP53
#> 4: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 5: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 6: chr17_7441178_C_T_b38 rs4151125 ENSG00000141510.16 TP53
#> tissueSiteDetail pValue nes datasetId
#> 1: Adipose - Subcutaneous 1.00467e-05 -0.403825 gtex_v8
#> 2: Adipose - Subcutaneous 8.68606e-10 -0.765786 gtex_v8
#> 3: Adipose - Subcutaneous 1.34916e-05 -0.401123 gtex_v8
#> 4: Cells - Cultured fibroblasts 9.07463e-06 -0.473760 gtex_v8
#> 5: Esophagus - Mucosa 5.18785e-07 -0.729226 gtex_v8
#> 6: Kidney - Cortex 7.27802e-07 -0.541302 gtex_v8Query eQTL associations with a variant-gene pair:
查询 eQTL 与变异-基因对的关联：
eQTL_sig4 <- xQTLquery_eqtlSig(variantName="rs1641513", genes="TP53")
eQTL_sig4 <- xQTLquery_eqtlSig(variantName="chr1_1667948_A_G_b38",
genes="SLC35E2B", tissueSiteDetail="Kidney - Cortex")eQTL_sig4#> variantId snpId gencodeId geneSymbol
#> 1: chr1_1667948_A_G_b38 rs368438548 ENSG00000189339.11 SLC35E2B
#> tissueSiteDetail pValue nes datasetId
#> 1: Kidney - Cortex 7.21369e-14 -1.05597 gtex_v8Multi-tissue eQTL metasoft results for a given gene and variant can be also queried using xQTLquery_eqtl, the results include: m-value (mValue), normalized effect size (nes), p-value (pValue) and standard error (se).
也可以使用 xQTLquery_eqtl 查询给定基因和变体的多组织 eQTL metasoft 结果，结果包括：m 值 （mValue）、归一化效应大小 （nes）、p 值 （pValue） 和标准误差 （se）。
# Query with a gene symbol:
eqtlMeta <- xQTLquery_eqtl(gene="TP53")
# Query with a variant-gene pair:
eqtlMeta <- xQTLquery_eqtl(variantName="rs1641513",gene="TP53")head(eqtlMeta)#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 2: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 3: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 4: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 5: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 6: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> tissueSiteDetail pValue nes se mValue
#> 1: Adipose - Subcutaneous 0.00992404 0.1065590 0.0411719 0.988
#> 2: Adipose - Visceral (Omentum) 0.02456600 0.0985826 0.0436840 0.953
#> 3: Adrenal Gland 0.49990900 0.0580124 0.0858289 0.729
#> 4: Artery - Aorta 0.84236100 -0.0113147 0.0568473 0.670
#> 5: Artery - Coronary 0.51525500 0.0624194 0.0957326 0.745
#> 6: Artery - Tibial 0.01521470 0.1224370 0.0502740 0.963
#> datasetId
#> 1: gtex_v8
#> 2: gtex_v8
#> 3: gtex_v8
#> 4: gtex_v8
#> 5: gtex_v8
#> 6: gtex_v8Query sQTLs: 查询 sQTL：
Query sQTL associations with rsid:
使用 rsid 查询 sQTL 关联：
sQTL_sig1 <- xQTLquery_sqtlSig(variantName="rs201327123")
sQTL_sig1 <- xQTLquery_sqtlSig(variantName="chr1_14677_G_A_b38", tissueSiteDetail="Whole Blood")sQTL_sig1#> variantId snpId gencodeId geneSymbol
#> 1: chr1_14677_G_A_b38 rs201327123 ENSG00000227232.5 WASH7P
#> phenotypeId tissueSiteDetail pValue
#> 1: chr1:15947:16607:clu_40980:ENSG00000227232.5 Whole Blood 7.14888e-08
#> nes datasetId
#> 1: 0.756834 gtex_v8Query sQTL associations with gene symbol and gencode ID:
查询带有基因符号和基因编码 ID 的 sQTL 关联：
#> variantId snpId gencodeId geneSymbol
#> 1: chr3_37136656_CAAAGA_C_b38 rs200076067 ENSG00000076242.14 MLH1
#> 2: chr3_37282912_C_T_b38 rs112128385 ENSG00000076242.14 MLH1
#> 3: chr1_1259424_T_C_b38 rs11804831 ENSG00000160072.19 ATAD3B
#> 4: chr1_1274256_A_G_b38 rs3737722 ENSG00000160072.19 ATAD3B
#> 5: chr1_1274972_A_G_b38 rs11260575 ENSG00000160072.19 ATAD3B
#> ---
#> 6330: chr1_1532105_T_C_b38 rs1987191 ENSG00000160072.19 ATAD3B
#> 6331: chr1_1533018_T_C_b38 rs6695186 ENSG00000160072.19 ATAD3B
#> 6332: chr1_1533095_G_A_b38 rs6677993 ENSG00000160072.19 ATAD3B
#> 6333: chr1_1533178_A_G_b38 rs6694773 ENSG00000160072.19 ATAD3B
#> 6334: chr1_1533253_C_T_b38 rs6690064 ENSG00000160072.19 ATAD3B
#> phenotypeId
#> 1: chr3:37040294:37047519:clu_44299:ENSG00000076242.14
#> 2: chr3:37040294:37047519:clu_44299:ENSG00000076242.14
#> 3: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> 4: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> 5: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> ---
#> 6330: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6331: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6332: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6333: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6334: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> tissueSiteDetail pValue nes datasetId
#> 1: Adipose - Subcutaneous 4.23971e-07 1.224370 gtex_v8
#> 2: Adipose - Subcutaneous 7.92886e-08 1.234820 gtex_v8
#> 3: Adipose - Subcutaneous 2.63274e-06 -0.334712 gtex_v8
#> 4: Adipose - Subcutaneous 1.92720e-06 -0.405750 gtex_v8
#> 5: Adipose - Subcutaneous 1.74607e-06 -0.389751 gtex_v8
#> ---
#> 6330: Whole Blood 3.35898e-07 -0.589917 gtex_v8
#> 6331: Whole Blood 4.09835e-06 -0.483704 gtex_v8
#> 6332: Whole Blood 2.61330e-07 -0.601543 gtex_v8
#> 6333: Whole Blood 5.63455e-07 -0.581156 gtex_v8
#> 6334: Whole Blood 3.35898e-07 -0.589917 gtex_v8Query sQTL associations with the variant-genes pair:
查询 sQTL 与 variant-genes 对的关联：
#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7465085_A_G_b38 rs546057177 ENSG00000141510.16 TP53
#> phenotypeId tissueSiteDetail
#> 1: chr17:7669690:7670609:clu_13833:ENSG00000141510.16 Lung
#> pValue nes datasetId
#> 1: 1.29439e-05 -0.566684 gtex_v8xQTLs Download xQTLs 下载
eQTL Download: eQTL 下载：
Download all eQTL associations for MLH1-rs13315355 pair in all tissues from all studies:
下载所有研究中所有组织中 MLH1-rs13315355 对的所有 eQTL 关联：
Download all eQTL associations for gene ATP11B in Muscle - Skeletal from GTEx_V8:
从 GTEx_V8 下载肌肉 - 骨骼中 ATP11B 基因的所有 eQTL 关联：
A more fast way to download eQTL association for a given gene is using “liLab” data source with paramater data_source="liLab" (only support GTEx tissues)
下载给定基因的 eQTL 关联的一种更快速的方法是使用带有参数 data_source=“liLab” 的 “liLab” 数据源（仅支持 GTEx 组织）
Download all eQTL associations for SNP rs11568818 in all tissues from all supported studies:
从所有支持的研究中下载所有组织中 SNP rs11568818 的所有 eQTL 关联：
Download all eQTL associations of SNP rs11568818 in Muscle - Skeletal from GTEx_V8:
从 GTEx_V8 下载 Muscle - Skeletal 中 SNP rs11568818 的所有 eQTL 关联：
Download all eQTL associations for gene ATP11B in CD4+ T cell from all supported studies:
从所有支持的研究中下载 CD4+ T 细胞中基因 ATP11B 的所有 eQTL 关联：
#> variantId snpId type maf beta chrom
#> 1: chr11_101531348_T_C_b38 rs4254048 SNP 0.3097830 0.0909405 11
#> 2: chr11_101531533_A_G_b38 rs11224820 SNP 0.1548910 0.0891349 11
#> 3: chr11_101532218_A_G_b38 rs145907949 SNP 0.0135870 -0.5316370 11
#> 4: chr11_101532331_A_G_b38 rs138388841 SNP 0.0135870 0.1777300 11
#> 5: chr11_101532593_G_A_b38 rs61916052 SNP 0.0108696 0.1754850 11
#> ---
#> 19131: chr11_103529577_C_A_b38 rs12365191 SNP 0.0674157 0.4218230 11
#> 19132: chr11_103529693_T_TTGTG_b38 rs147237734 INDEL 0.3595510 0.1532910 11
#> 19133: chr11_103529825_T_C_b38 rs34949425 SNP 0.2247190 -0.1864580 11
#> 19134: chr11_103530122_T_C_b38 rs4754958 SNP 0.3089890 0.7059100 11
#> 19135: chr11_103530486_C_G_b38 rs17380432 SNP 0.3314610 -0.1633750 11
#> pos ref alt se median_tpm pValue totalAlleles
#> 1: 101531348 T C 0.210025 5.637 0.6655640 368
#> 2: 101531533 A G 0.256792 5.637 0.7289380 368
#> 3: 101532218 A G 0.837931 5.637 0.5266310 368
#> 4: 101532331 A G 0.807995 5.637 0.8261630 368
#> 5: 101532593 G A 1.179750 5.637 0.8819290 368
#> ---
#> 19131: 103529577 C A 0.438372 0.000 0.3390160 178
#> 19132: 103529693 T TTGTG 0.242597 0.000 0.5293910 178
#> 19133: 103529825 T C 0.273032 0.000 0.4967640 178
#> 19134: 103530122 T C 0.282450 0.000 0.0146332 178
#> 19135: 103530486 C G 0.246976 0.000 0.5103180 178
#> allelCounts imputationR2 condition molecular_trait_id
#> 1: 114 0.94063 None ENSG00000137673
#> 2: 57 0.95629 None ENSG00000137673
#> 3: 5 0.94880 None ENSG00000137673
#> 4: 6 0.69826 None ENSG00000137673
#> 5: 4 0.73096 None ENSG00000137673
#> ---
#> 19131: 12 0.97970 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19132: 63 0.87166 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19133: 40 0.98203 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19134: 55 0.98227 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19135: 59 0.98326 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> gene_id study_id tissue tissue_label
#> 1: ENSG00000137673 GENCORD CL_0000624 T cell
#> 2: ENSG00000137673 GENCORD CL_0000624 T cell
#> 3: ENSG00000137673 GENCORD CL_0000624 T cell
#> 4: ENSG00000137673 GENCORD CL_0000624 T cell
#> 5: ENSG00000137673 GENCORD CL_0000624 T cell
#> ---
#> 19131: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19132: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19133: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19134: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19135: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> qtl_group geneSymbol gencodeId_GTEX_v8
#> 1: T-cell MMP7 ENSG00000137673.8
#> 2: T-cell MMP7 ENSG00000137673.8
#> 3: T-cell MMP7 ENSG00000137673.8
#> 4: T-cell MMP7 ENSG00000137673.8
#> 5: T-cell MMP7 ENSG00000137673.8
#> ---
#> 19131: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19132: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19133: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19134: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19135: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8sQTL Download: sQTL 下载：
Download all sQTL associations for gene MMP7 and TP53 in Lung:
下载 Lung 中基因 MMP7 和 TP53 的所有 sQTL 关联：
#> rsid clu_name pValue beta se gencodeId
#> 1: rs4254048 clu_9701 0.4562150 0.05216700 0.0699585 ENSG00000137673.8
#> 2: rs11224820 clu_9701 0.0334606 -0.18979000 0.0889982 ENSG00000137673.8
#> 3: rs138388841 clu_9701 0.6221730 0.08717970 0.1768040 ENSG00000137673.8
#> 4: rs61916052 clu_9701 0.4701730 0.13079100 0.1809620 ENSG00000137673.8
#> 5: rs78752240 clu_9701 0.3274160 -0.33715300 0.3439250 ENSG00000137673.8
#> ---
#> 36276: rs59885278 clu_13833 0.2352270 0.22514800 0.1894450 ENSG00000141510.16
#> 36277: rs73251879 clu_13833 0.9783160 0.00368261 0.1354170 ENSG00000141510.16
#> 36278: rs58698225 clu_13833 0.9029850 0.00683635 0.0560565 ENSG00000141510.16
#> 36279: rs12935932 clu_13833 0.8615360 -0.01098430 0.0629434 ENSG00000141510.16
#> 36280: rs4346241 clu_13833 0.0140373 -0.16665600 0.0676048 ENSG00000141510.163’aQTL Download: 3'aQTL 下载：
Download all 3’aQTL associations for gene MMP7 in Lung:
下载 Lung 中 MMP7 基因的所有 3'aQTL 关联：
#> rsid maf pValue beta se
#> 1: rs2701977 0.5743146 0.0007479838 -2.100113e-01 0.06186416
#> 2: rs1711402 0.8896104 0.0012343600 -3.024068e-01 0.09300488
#> 3: rs1784450 0.8896104 0.0014384863 -2.965600e-01 0.09248070
#> 4: rs948138 0.5512266 0.0015553106 -1.948009e-01 0.06118752
#> 5: chr11_102631148_C_T_b38 0.5808081 0.0017118558 -1.949774e-01 0.06179620
#> ---
#> 4178: rs2846715 0.5389611 0.9964685792 2.647676e-04 0.05978774
#> 4179: rs2846342 0.5389611 0.9964685792 2.647676e-04 0.05978774
#> 4180: rs4254048 0.3145743 0.9993855679 5.160473e-05 0.06697517
#> 4181: rs7123862 0.6360347 0.9996407735 2.974098e-05 0.06602145
#> 4182: rs10895249 0.3831169 0.9999300442 5.476405e-06 0.06242669
#> mRNA gencodeId
#> 1: NM_002423.5 ENSG00000137673.8
#> 2: NM_002423.5 ENSG00000137673.8
#> 3: NM_002423.5 ENSG00000137673.8
#> 4: NM_002423.5 ENSG00000137673.8
#> 5: NM_002423.5 ENSG00000137673.8
#> ---
#> 4178: NM_002423.5 ENSG00000137673.8
#> 4179: NM_002423.5 ENSG00000137673.8
#> 4180: NM_002423.5 ENSG00000137673.8
#> 4181: NM_002423.5 ENSG00000137673.8
#> 4182: NM_002423.5 ENSG00000137673.8mQTL Download: mQTL 下载：
Download all mQTL associations with cgp_id “cg00000221” in Prostate:
下载前列腺中所有带有 cgp_id “cg00000221” 的 mQTL 关联：
#> variant_id gene maf pValue beta se
#> 1: chr17_48080661_G_A_b38 cg07625849 0.2238100 0.7905950 0.0295557 0.110913
#> 2: chr17_48080688_T_C_b38 cg07625849 0.2238100 0.0787432 0.2099310 0.117806
#> 3: chr17_48081171_T_C_b38 cg07625849 0.1380950 0.0706286 0.2153530 0.117448
#> 4: chr17_48081344_A_T_b38 cg07625849 0.0190476 0.6815340 -0.1598080 0.387928
#> 5: chr17_48081546_C_G_b38 cg07625849 0.2238100 0.0787432 0.2099310 0.117806
#> ---
#> 2774: chr17_49079069_C_G_b38 cg07625849 0.2238100 0.3348770 -0.1138980 0.117360
#> 2775: chr17_49079242_G_A_b38 cg07625849 0.0952381 0.1356170 0.2237770 0.148361
#> 2776: chr17_49079593_G_A_b38 cg07625849 0.0380952 0.3482250 -0.2615080 0.277058
#> 2777: chr17_49079687_A_T_b38 cg07625849 0.0142857 0.4095380 0.3410300 0.411232
#> 2778: chr17_49080066_G_A_b38 cg07625849 0.1809520 0.1526370 -0.1839900 0.127350hQTL Download: hQTL 下载：
Download all hQTL associations for H3K4ME1 in T cell:
下载 T 细胞中 H3K4ME1 的所有 hQTL 关联：
#> rsid gene maf pValue beta se
#> 1: rs950228 10:10458128:10465096 0.4850 0.3871 -0.12300 0.1422
#> 2: rs12783041 10:10458128:10465096 0.3850 0.4063 0.11590 0.1396
#> 3: rs7903944 10:10458128:10465096 0.4825 0.4623 -0.10580 0.1439
#> 4: rs10905556 10:10458128:10465096 0.4800 0.3548 -0.13040 0.1409
#> 5: rs34488055 10:10458128:10465096 0.1275 0.7625 -0.06456 0.2136
#> ---
#> 4209: rs72777637 10:10458128:10465096 0.0550 0.8334 0.06993 0.3325
#> 4210: rs2440112 10:10458128:10465096 0.7375 0.5641 -0.10610 0.1840
#> 4211: rs77085282 10:10458128:10465096 0.0525 0.5223 0.20470 0.3199
#> 4212: rs7068574 10:10458128:10465096 0.1900 0.8650 -0.03029 0.1782
#> 4213: rs2499927 10:10458128:10465096 0.0525 0.2223 0.42320 0.3468
#> variantId
#> 1: 10:9458147_A_G
#> 2: 10:9459295_T_C
#> 3: 10:9459626_C_T
#> 4: 10:9460058_C_T
#> 5: 10:9463102_A_G
#> ---
#> 4209: 10:11461313_T_C
#> 4210: 10:11462143_T_C
#> 4211: 10:11464056_T_C
#> 4212: 10:11464106_G_C
#> 4213: 10:11464602_T_ASingle-cell eQTLs (sc-eQTLs) Download:
单细胞 eQTL （sc-eQTLs） 下载：
Download Cell-type eQTLs for gene TP53 in B cell from study Resztak2022biorxiv:
从研究 Resztak2022biorxiv 中下载 B 细胞中基因 TP53 的细胞型 eQTL：
#> beta cellType chromosome geneSymbol pValue pos
#> 1: -0.0120341 B Cell chr17 TP53 0.894893 7639177
#> 2: -0.0122527 B Cell chr17 TP53 0.892879 7639273
#> 3: -0.0866685 B Cell chr17 TP53 0.340513 7639553
#> 4: -0.0135121 B Cell chr17 TP53 0.881551 7639699
#> 5: -0.0181303 B Cell chr17 TP53 0.839595 7640154
#> ---
#> 260: -0.162146 B Cell chr17 TP53 0.0816707 7697870
#> 261: 0.13485 B Cell chr17 TP53 0.235491 7719119
#> 262: -0.121788 B Cell chr17 TP53 0.303225 7722187
#> 263: 0.070017 B Cell chr17 TP53 0.602875 7722656
#> 264: 0.18766 B Cell chr17 TP53 0.0818137 7724742
#> qtlType se snpId
#> 1: Cell-type-specific eQTL 0.0910877781405 rs2430948
#> 2: Cell-type-specific eQTL 0.0909884473621 rs1642795
#> 3: Cell-type-specific eQTL 0.0909282976755 rs1642796
#> 4: Cell-type-specific eQTL 0.0906832041021 rs1642797
#> 5: Cell-type-specific eQTL 0.0895714697899 rs12450254
#> ---
#> 260: Cell-type-specific eQTL 0.0931299007474 rs1393370347
#> 261: Cell-type-specific eQTL 0.113669645877 rs373872446
#> 262: Cell-type-specific eQTL 0.11829336382 rs1052202011
#> 263: Cell-type-specific eQTL 0.134578050437 rs8070743
#> 264: Cell-type-specific eQTL 0.107834576496 rs370880934
#> study variantId
#> 1: Resztak2022biorxiv_qtl rs2430948
#> 2: Resztak2022biorxiv_qtl rs1642795
#> 3: Resztak2022biorxiv_qtl rs1642796
#> 4: Resztak2022biorxiv_qtl rs1642797
#> 5: Resztak2022biorxiv_qtl rs12450254
#> ---
#> 260: Resztak2022biorxiv_qtl rs1393370347
#> 261: Resztak2022biorxiv_qtl rs373872446
#> 262: Resztak2022biorxiv_qtl rs1052202011
#> 263: Resztak2022biorxiv_qtl rs8070743
#> 264: Resztak2022biorxiv_qtl rs370880934Query details of gene, variant, tissue and samples in GTEx:
在 GTEx 中查询基因、变异、组织和样本的详细信息：
Query gene details with gene symbols, versioned or unversioned gencode ID:
使用基因符号、版本化或未版化的 gencode ID 查询基因详细信息：
#> genes genesUpper geneSymbol gencodeId
#> 1: ENSG00000210195.2 ENSG00000210195.2 MT-TT ENSG00000210195.2
#> 2: ENSG00000078808 ENSG00000078808 SDF4 ENSG00000078808.16
#> entrezGeneId geneType chromosome start end strand tss
#> 1: NA Mt tRNA chrM 15888 15953 + 15888
#> 2: 51150 protein coding chr1 1216908 1232031 - 1232031
#> gencodeVersion genomeBuild
#> 1: v26 GRCh38/hg38
#> 2: v26 GRCh38/hg38
#> description
#> 1: mitochondrially encoded tRNA threonine [Source:HGNC Symbol;Acc:HGNC:7499]
#> 2: stromal cell derived factor 4 [Source:HGNC Symbol;Acc:HGNC:24188]Query variants using dbSNP ID or variant ID:
使用 dbSNP ID 或变体 ID 查询变体：
> variantId snpId b37VariantId chromosome pos ref alt
#> 1: chr1_1102708_G_C_b38 rs66622470 1_1038088_G_C_b37 chr1 1102708 G C
#> datasetId maf01 shorthand
#> 1: gtex_v8 TRUE NAQuery tissue using tissue name:
使用组织名称查询组织：
#> colorHex colorRgb datasetId eGeneCount eqtlAgeMaxFemale eqtlAgeMaxMale
#> 1: EEEE00 238,238,0 gtex_v8 3726 70 70
#> 2: EEEE00 238,238,0 gtex_v8 5640 70 70
#> 3: EEEE00 238,238,0 gtex_v8 8362 70 70
#> 4: EEEE00 238,238,0 gtex_v8 10027 70 70
#> 5: EEEE00 238,238,0 gtex_v8 11240 70 70
#> 6: EEEE00 238,238,0 gtex_v8 9082 70 70
#> 7: EEEE00 238,238,0 gtex_v8 7335 70 70
#> 8: EEEE00 238,238,0 gtex_v8 5517 70 70
#> 9: EEEE00 238,238,0 gtex_v8 5499 70 70
#> 10: EEEE00 238,238,0 gtex_v8 8198 70 70
#> 11: EEEE00 238,238,0 gtex_v8 6902 70 70
#> 12: EEEE00 238,238,0 gtex_v8 4483 70 70
#> 13: EEEE00 238,238,0 gtex_v8 3301 70 70
#> eqtlAgeMeanFemale eqtlAgeMeanMale eqtlAgeMinFemale eqtlAgeMinMale
#> 1: 57.6 58.2 28 20
#> 2: 57.2 58.2 24 20
#> 3: 56.8 58.5 24 22
#> 4: 57.5 57.5 24 20
#> 5: 58.7 56.7 24 20
#> 6: 58.2 57.3 24 20
#> 7: 59.1 58.6 28 20
#> 8: 58.9 58.2 28 20
#> 9: 59.6 58.7 28 20
#> 10: 57.7 58.2 24 20
#> 11: 58.4 58.1 28 20
#> 12: 58.2 58.4 28 22
#> 13: 56.2 58.6 24 20
#> eqtlSampleCountFemale eqtlSampleCountMale expressedGeneCount hasEGenes
#> 1: 37 92 28196 TRUE
#> 2: 42 105 28921 TRUE
#> 3: 52 142 29230 TRUE
#> 4: 51 124 29538 TRUE
#> 5: 58 151 30106 TRUE
#> 6: 64 141 29560 TRUE
#> 7: 48 127 29132 TRUE
#> 8: 49 116 28625 TRUE
#> 9: 47 123 29502 TRUE
#> 10: 55 147 29339 TRUE
#> 11: 42 128 28335 TRUE
#> 12: 48 78 28352 TRUE
#> 13: 33 81 28050 TRUE
#> hasSGenes mappedInHubmap rnaSeqAgeMaxFemale rnaSeqAgeMaxMale
#> 1: TRUE FALSE 70 70
#> 2: TRUE FALSE 70 70
#> 3: TRUE FALSE 70 70
#> 4: TRUE FALSE 70 70
#> 5: TRUE FALSE 70 70
#> 6: TRUE FALSE 70 70
#> 7: TRUE FALSE 70 70
#> 8: TRUE FALSE 70 70
#> 9: TRUE FALSE 70 70
#> 10: TRUE FALSE 70 70
#> 11: TRUE FALSE 70 70
#> 12: TRUE FALSE 70 70
#> 13: TRUE FALSE 70 70
#> rnaSeqAgeMeanFemale rnaSeqAgeMeanMale rnaSeqAgeMinFemale rnaSeqAgeMinMale
#> 1: 57.2 58.9 28 20
#> 2: 57.2 58.8 24 20
#> 3: 56.9 59.2 24 22
#> 4: 57.3 58.5 24 20
#> 5: 58.3 57.3 24 20
#> 6: 57.8 58.2 24 20
#> 7: 58.7 59.1 28 20
#> 8: 58.3 58.8 28 20
#> 9: 59.3 59.0 28 20
#> 10: 57.7 58.8 24 20
#> 11: 58.4 58.5 28 20
#> 12: 58.1 59.7 28 22
#> 13: 56.2 59.3 24 20
#> rnaSeqAndGenotypeSampleCount rnaSeqSampleCount rnaSeqSampleCountFemale
#> 1: 129 152 45
#> 2: 147 176 48
#> 3: 194 246 63
#> 4: 175 215 58
#> 5: 209 241 67
#> 6: 205 255 74
#> 7: 175 209 56
#> 8: 165 197 54
#> 9: 170 202 55
#> 10: 202 246 64
#> 11: 170 205 49
#> 12: 126 159 57
#> 13: 114 139 38
#> rnaSeqSampleCountMale sGeneCount
#> 1: 107 892
#> 2: 128 1238
#> 3: 183 1809
#> 4: 157 2397
#> 5: 174 2786
#> 6: 181 2048
#> 7: 153 1684
#> 8: 143 1185
#> 9: 147 1414
#> 10: 182 1881
#> 11: 156 1350
#> 12: 102 1144
#> 13: 101 814
#> samplingSite
#> 1: Amygdala (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 2: Anterior cingulate cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 3: Caudate (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 4: Cerebellar hemisphere (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 5: Right cerebellum (sampled at donor collection site and preserved in PAXgene fixative).
#> 6: Right cerebral frontal pole cortex (sampled at donor collection site and preserved in PAXgene fixative).
#> 7: Right cerebral frontal pole cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 8: Hippocampus (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 9: Hypothalamus (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 10: Nucleus accumbens basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 11: Putamen basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 12: Spinal cord (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 13: Substantia nigra (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> tissueSite tissueSiteDetail tissueSiteDetailAbbr
#> 1: Brain Brain - Amygdala BRNAMY
#> 2: Brain Brain - Anterior cingulate cortex (BA24) BRNACC
#> 3: Brain Brain - Caudate (basal ganglia) BRNCDT
#> 4: Brain Brain - Cerebellar Hemisphere BRNCHB
#> 5: Brain Brain - Cerebellum BRNCHA
#> 6: Brain Brain - Cortex BRNCTXA
#> 7: Brain Brain - Frontal Cortex (BA9) BRNCTXB
#> 8: Brain Brain - Hippocampus BRNHPP
#> 9: Brain Brain - Hypothalamus BRNHPT
#> 10: Brain Brain - Nucleus accumbens (basal ganglia) BRNNCC
#> 11: Brain Brain - Putamen (basal ganglia) BRNPTM
#> 12: Brain Brain - Spinal cord (cervical c-1) BRNSPC
#> 13: Brain Brain - Substantia nigra BRNSNG
#> tissueSiteDetailId uberonId
#> 1: Brain_Amygdala 0001876
#> 2: Brain_Anterior_cingulate_cortex_BA24 0009835
#> 3: Brain_Caudate_basal_ganglia 0001873
#> 4: Brain_Cerebellar_Hemisphere 0002037
#> 5: Brain_Cerebellum 0002037
#> 6: Brain_Cortex 0001870
#> 7: Brain_Frontal_Cortex_BA9 0009834
#> 8: Brain_Hippocampus 0001954
#> 9: Brain_Hypothalamus 0001898
#> 10: Brain_Nucleus_accumbens_basal_ganglia 0001882
#> 11: Brain_Putamen_basal_ganglia 0001874
#> 12: Brain_Spinal_cord_cervical_c-1 0006469
#> 13: Brain_Substantia_nigra 0002038Query sample using tissue name or sample ID:
使用组织名称或样本 ID 查询样本：
> ageBracket aliquotId autolysisScore dataType datasetId
#> 1: 60-69 SM-5EGGQ Mild RNASEQ gtex_v8
#> 2: 50-59 SM-DO12B <NA> RNASEQ gtex_v8
#> 3: 60-69 SM-DO93H <NA> RNASEQ gtex_v8
#> 4: 50-59 SM-5IFGI Mild EXCLUDE gtex_v8
#> hardyScale ischemicTime ischemicTimeGroup
#> 1: Fast death - natural causes 891 601 - 900
#> 2: Fast death - natural causes 864 601 - 900
#> 3: Fast death - natural causes 587 301 - 600
#> 4: Fast death - natural causes 1129 901 - 1200
#> pathologyNotes rin
#> 1: 2 pieces, congestion 6.8
#> 2: <NA> 7.1
#> 3: <NA> 7.1
#> 4: 2 pieces; cirrhosis, steatosis, Mallory hyaline c/w alcoholic cirrhosis 6.2
#> sampleId sex subjectId tissueSampleId
#> 1: GTEX-11DXY-0526-SM-5EGGQ male GTEX-11DXY GTEX-11DXY-0526
#> 2: GTEX-11NUK-0011-R4a-SM-DO12B male GTEX-11NUK GTEX-11NUK-0011-R4a
#> 3: GTEX-11ONC-0011-R4b-SM-DO93H male GTEX-11ONC GTEX-11ONC-0011-R4b
#> 4: GTEX-13OVJ-1026-SM-5IFGI female GTEX-13OVJ GTEX-13OVJ-1026
#> tissueSiteDetail tissueSiteDetailId uberonId
#> 1: Liver Liver 0001114
#> 2: Brain - Amygdala Brain_Amygdala 0001876
#> 3: Brain - Amygdala Brain_Amygdala 0001876
#> 4: Liver Liver 0001114xQTL expression download xQTL 表达下载
Download normalized expression of gene for a eQTL pair.
下载 eQTL 对的基因标准化表达。
Download exp with variant-gene pair in different tissues:
下载不同组织中变异基因对的 exp：
Download expression using variant ID and gencode ID:
使用变体 ID 和 gencode ID 下载表达式：
#> normExp genotypes
#> 1: -2.1600444 0
#> 2: 0.1509692 0
#> 3: 0.7464682 0
#> 4: -0.2613195 0
#> 5: 0.9212440 0
#> ---
#> 320: 0.9944579 0
#> 321: -0.9450852 0
#> 322: -0.7566981 0
#> 323: 1.3266775 0
#> 324: 0.8750651 0Download normalized intron-excision ratio of intron for a sQTL pair.
下载 sQTL 对的内含子的标准化内含子切除比。
Download normalized intron-excision ratio in different tissues:
下载不同组织中的标准化内含子切除比：
Dowload normalized intron-excision ratio using variant ID:
使用变体 ID 的 Dowload 归一化内含子切除比：
#> normExp genotypes
#> 1: 1.39907974 0
#> 2: -0.02638638 0
#> 3: 1.43450451 1
#> 4: 0.25182051 0
#> 5: -1.94683842 2
#> ---
#> 577: 1.82050424 2
#> 578: 1.24869651 1
#> 579: 0.61319702 0
#> 580: -2.59815685 1
#> 581: -1.69950516 1eGene/sGene download eGene/sGene 下载
Download details of eGenes (eQTL Genes) for a specified gene or a tissue.
下载指定基因或组织的 eGenes （eQTL Genes） 详细信息。
#> gencodeId geneSymbol entrezGeneId geneType chromosome start
#> 1: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 2: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 3: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 4: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 5: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 6: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 7: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> end tss log2AllelicFoldChange empiricalPValue pValue
#> 1: 7687550 7687550 -0.680804 4.94757e-06 8.68606e-10
#> 2: 7687550 7687550 -0.500061 2.63392e-02 9.07463e-06
#> 3: 7687550 7687550 -0.501278 2.00743e-03 5.18785e-07
#> 4: 7687550 7687550 -0.359329 1.43349e-03 6.52895e-07
#> 5: 7687550 7687550 -1.243570 1.55063e-03 5.70716e-07
#> 6: 7687550 7687550 -0.541348 1.38551e-06 2.05198e-10
#> 7: 7687550 7687550 -0.550911 2.00129e-07 3.00426e-11
#> pValueThreshold qValue tissueSiteDetail datasetId
#> 1: 1.26507e-04 3.94849e-06 Adipose - Subcutaneous gtex_v8
#> 2: 1.52146e-04 1.03629e-02 Cells - Cultured fibroblasts gtex_v8
#> 3: 1.13047e-04 1.25547e-03 Esophagus - Mucosa gtex_v8
#> 4: 5.80918e-06 2.32936e-02 Kidney - Cortex gtex_v8
#> 5: 3.88929e-05 2.94618e-03 Pituitary gtex_v8
#> 6: 1.18255e-04 1.28231e-06 Skin - Not Sun Exposed (Suprapubic) gtex_v8
#> 7: 1.60112e-04 1.50952e-07 Skin - Sun Exposed (Lower leg) gtex_v8Download details of sGenes (sQTL Genes) for a specified gene or a tissue.
下载指定基因或组织的 sGenes （sQTL Genes） 的详细信息。
#> gencodeId geneSymbol entrezGeneId geneType chromosome start
#> 1: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 2: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 3: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 4: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 5: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 6: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 7: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> end tss log2AllelicFoldChange empiricalPValue pValue
#> 1: 7687550 7687550 -0.680804 4.94757e-06 8.68606e-10
#> 2: 7687550 7687550 -0.500061 2.63392e-02 9.07463e-06
#> 3: 7687550 7687550 -0.501278 2.00743e-03 5.18785e-07
#> 4: 7687550 7687550 -0.359329 1.43349e-03 6.52895e-07
#> 5: 7687550 7687550 -1.243570 1.55063e-03 5.70716e-07
#> 6: 7687550 7687550 -0.541348 1.38551e-06 2.05198e-10
#> 7: 7687550 7687550 -0.550911 2.00129e-07 3.00426e-11
#> pValueThreshold qValue tissueSiteDetail datasetId
#> 1: 1.26507e-04 3.94849e-06 Adipose - Subcutaneous gtex_v8
#> 2: 1.52146e-04 1.03629e-02 Cells - Cultured fibroblasts gtex_v8
#> 3: 1.13047e-04 1.25547e-03 Esophagus - Mucosa gtex_v8
#> 4: 5.80918e-06 2.32936e-02 Kidney - Cortex gtex_v8
#> 5: 3.88929e-05 2.94618e-03 Pituitary gtex_v8
#> 6: 1.18255e-04 1.28231e-06 Skin - Not Sun Exposed (Suprapubic) gtex_v8
#> 7: 1.60112e-04 1.50952e-07 Skin - Sun Exposed (Lower leg) gtex_v8Gene expression download 基因表达下载
Download normalized gene expression at the sample level in a specified tissue:
下载指定组织中样品水平的标准化基因表达：
Download gene expression with a genecode ID:
下载带有基因编码 ID 的基因表达：
Download gene expression into a SummarizedExperiment object:
将基因表达下载到 SummarizedExperiment 对象中：
Download gene expression profiles for multiple genes:
下载多个基因的基因表达谱：
Download using versioned and unversioned gencode Id.
使用版本控制和未版本控制的 gencode ID 下载。
> gencodeId genes geneSymbol datasetId tissueSiteDetailId
#> 1 ENSG00000141510.16 ENSG00000141510.16 TP53 gtex_v8 Artery_Coronary
#> 2 ENSG00000008130.15 ENSG00000008130.15 NADK gtex_v8 Artery_Coronary
#> 3 ENSG00000078808.16 ENSG00000078808 SDF4 gtex_v8 Artery_Coronary
#> unit genesUpper GTEX-1117F-0626-SM-5N9CS GTEX-1122O-0426-SM-5H12G
#> 1 TPM ENSG00000141510.16 27.83 16.88
#> 2 TPM ENSG00000008130.15 77.78 60.54
#> 3 TPM ENSG00000078808.16 210.60 205.60
#> GTEX-117YX-1726-SM-5GZZS GTEX-11DXX-0826-SM-5GZZP GTEX-11DXY-1126-SM-5987W
#> 1 20.25 24.36 20.53
#> 2 69.14 62.15 31.90
#> 3 203.60 184.10 188.60Download median expression of all samples for specified genes across tissues.
下载组织中指定基因的所有样品的中位表达。
#> gencodeId geneSymbol median tissueSiteDetail
#> 1: ENSG00000128604.19 IRF5 8.53482 Adipose - Subcutaneous
#> 2: ENSG00000128604.19 IRF5 6.12789 Adipose - Visceral (Omentum)
#> 3: ENSG00000128604.19 IRF5 4.67700 Adrenal Gland
#> 4: ENSG00000128604.19 IRF5 5.29194 Artery - Aorta
#> 5: ENSG00000128604.19 IRF5 6.60034 Artery - Coronary
#> ---
#> 104: ENSG00000141510.16 TP53 14.82610 Testis
#> 105: ENSG00000141510.16 TP53 19.66310 Thyroid
#> 106: ENSG00000141510.16 TP53 29.49970 Uterus
#> 107: ENSG00000141510.16 TP53 25.29200 Vagina
#> 108: ENSG00000141510.16 TP53 7.69810 Whole Blood
#> entrezGeneId geneType chromosome start end strand
#> 1: 3663 protein coding chr7 128937612 128950035 +
#> 2: 3663 protein coding chr7 128937612 128950035 +
#> 3: 3663 protein coding chr7 128937612 128950035 +
#> 4: 3663 protein coding chr7 128937612 128950035 +
#> 5: 3663 protein coding chr7 128937612 128950035 +
#> ---
#> 104: 7157 protein coding chr17 7661779 7687550 -
#> 105: 7157 protein coding chr17 7661779 7687550 -
#> 106: 7157 protein coding chr17 7661779 7687550 -
#> 107: 7157 protein coding chr17 7661779 7687550 -
#> 108: 7157 protein coding chr17 7661779 7687550 -
#> tss
#> 1: 128937612
#> 2: 128937612
#> 3: 128937612
#> 4: 128937612
#> 5: 128937612
#> ---
#> 104: 7687550
#> 105: 7687550
#> 106: 7687550
#> 107: 7687550
#> 108: 7687550
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