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Browser: BROWSER provides data about Tissue-specific genes, Tissue-specific hypermethylation sites, Tissue-specific hypomethylation sites.
| Dataset | Description | Source |
| Tissue-specific genes (TSGs) | Genes that specifically express in only one tissue. Noramlly, specific gene has a high SPMadjust value and high Tscore value, e.g. SPMadjust >= 0.8, Tscore >= 0.6. | GEO, HPA, GTEX, RNASeq Atlas |
| Tissue-specific hypermethylation (TSHMs) | Methylation sites that expressed only in one tissue with a frequency greater than 0.7 . SPMadjust >= 0.8, Tscore >= 0.6. | ENCODE, ROADMAP, EWAS Data Hub, GEO |
| Tissue-specific hypomethylation (TSUMs) | Methylation sites that are not expressed or are underexpressed in a tissue with a frequency lower than 0.3 . SPMadjust >= 0.8, Tscore >= 0.6. | ENCODE, ROADMAP, EWAS Data Hub, GEO |
| Tissue-specific proteins (TSPs) | Proteins that specifically express in only one tissue. SPMadjust >= 0.8, Tscore >= 0.6. | HPA, GTEX, PRIDE |
| Housekeeping hypermethylation sites (HKHMs) | The HKHMs which were consistently highly methylated across almost all tissues. methylation level > 0.7 and Tscore >= 0.6. | ENCODE, ROADMAP, EWAS Data Hub, GEO |
| Housekeeping hypomethylation sites (HKUMs) | The HKUMs which were nearly unmethylation or hypomethylation in most tissues. methylation level < 0.3 and Tscore >= 0.6. | ENCODE, ROADMAP, EWAS Data Hub, GEO |
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Datasets for download
Datasets for download
| Dataset | Description | Source | Download |
| Tissue-specific hypermethylation sites (TSHM) | TSHMs at the system/tissue/sub-tissue level | TSHMs.csv | Download |
| Tissue-specific hypomethylation sites (TSUMs) | TSUMs at the system/tissue/sub-tissue level | TSUMs.csv | Download |
| Tissue-specific genes (TSGs) | TSGs at the system/tissue/sub-tissue level | TSGs.csv | Download |
| Tissue-specific proteins (TSPs) | TSPs at the system/tissue/sub-tissue level | TSPs.csv | Download |
| Housekeeping hypermethylation sites (HKHMs) | HKHMs at the tissue level | HKHMs.csv | Download |
| Housekeeping hypomethylation sites (HKUMs) | HKUMs at the tissue level | HKUMs.csv | Download |
- Xiao SJ, Zhang C, Zou Q, Ji ZL. TiSGeD: a database for tissue-specific genes. Bioinformatics 2010;26:1273-5.
- Xiong Z, Li M, Yang F, Ma Y, Sang J, Li R, et al. EWAS Data Hub: a resource of DNA methylation array data and metadata. Nucleic Acids Res 2020;48:D890-D5.
- Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.
- Roadmap Epigenomics C, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature 2015;518:317-30.
- Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res 2013;41:D991-5.
- Consortium GT. The Genotype-Tissue Expression (GTEx) project. Nat Genet 2013;45:580-5.
- Sjostedt E, Zhong W, Fagerberg L, Karlsson M, Mitsios N, Adori C, et al. An atlas of the protein-coding genes in the human, pig, and mouse brain. Science 2020;367.
- Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics 2012;28:1184-5.
- Perez-Riverol Y, Bai J, Bandla C, Garcia-Seisdedos D, Hewapathirana S, Kamatchinathan S, et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res 2022;50:D543-D52.