Last build: Dec. 3, 2020 Reference Genome: GRCh38
Data availability: National Bioscience Database Center (NBDC) Human Database (http://humandbs.biosciencedbc.jp/en/) Research ID of hum0214
Gene expression data accession number : E-GEAD-397
Conditional eQTL data (significant associations) accession number :E-GEAD-398
Nominal eQTL statistics (including non-significant associations) accession number: E-GEAD-420
Q: What is ImmuNexUT?
ImmuNexUT (Immune Cell Gene Expression Atlas from the University of Tokyo) is a gene expression and eQTL atlas from 28 types of immune cells isolated from 10 distinct human immune mediated diseases, as well as healthy donors. The expanding atlas consists of 9,852 immune cell samples from 416 donors at its first release in 2021.
Q: I could not find my gene of interest.
Ans: We used GENCODE version 27 annotations for gene expression quantification, and only gene symbols, such as STAT1, are searchable.
Q: I queried my gene of interest. However, only data of healthy individuals were shown.
Ans: Genes with low expression were filtered out in inter-disease comparative analysis, and only the expression data of healthy individuals are shown for these genes.
Q: How was the expression data normalized in the gene expression database of health and immune mediated diseases?
Ans: After filtering out low-expressed genes, gene expression data was normalized with voom transformation of limma package with sex, age, prednisolone dosage and study phase as covariates.
Q: Can I search eQTL database for my SNP of interest?
Ans: Yes, you can query eQTLs by SNP IDs (dbSNP, version 146). Please search with SNP IDs, such as rs873458.
Q: What do eQTL results mean?
Ans: Significant eQTLs (FDR<0.05) are listed in the table. When the gene has >1,000 eQTLs, top 1,000 eQTLs are included. For each pair of eGene and eVariant, the cell type with the lowest P value and the corresponding P value are listed. For comparison of eQTL effects between cell types, please click on “eQTL plot” link in the table, which will enable you to see eQTL box plots of each cell type. In the eQTL box plots, normalized expression values are compared by eQTL genotypes. The numbers below box plots indicate the number of samples.
Q: Will new data be added in the future?
Ans: Yes, we are working on additional immune cell types and additional immune mediated diseases.
Q: Can I download the genome data?
Ans: No, because it could potentially be used to identify a specific person, Japanese regulations classify genotype data as personal information that may not be provided to third parties. Gene expression data and expression QTL data are available from the NBDC database above.
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This study was supported by Chugai Pharmaceutical Co., Ltd., Tokyo, Japan, the Center of Innovation Program from Japan Science and Technology Agency (JST), the Ministry of Education, Culture, Sports, and the Japan Agency for Medical Research and Development (AMED) (JP17ek0109103, 19ek0410047, and JP20ek0410074).
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