Brain - Substantia nigra

The list is GTEx's own ranking of the release's genes by median expression in this tissue, in the source's unit and order, from the dataset gtex_v10: the first page was read from the GTEx Portal API on 2026-09-09 and built into this site, and every page after it is read live when asked for. The read time is printed with every page because the licence asks for it.

The endpoint, in the API's own words: Returns top expressed genes for a specified tissue in a dataset, sorted by median expression. When the optional parameter filterMtGene is set to true, mitochondrial genes will be excluded from the results. [R26] The call sends that parameter as true, which is the endpoint's own default, so the mitochondrial genes are left out by the source's default and not by this site. The unit: Gene and transcript expression on the GTEx Portal are shown in Transcripts Per Million (TPM) [R25]. And the FAQ's own caution, which points at [R08]: It is not possible to directly compare these values across tissues. Unfortunately, no computational method can be applied for proper between-sample normalization across the diverse set of tissues represented in GTEx. [R25]

The material, in GTEx's words: The project collected samples from up to 54 non-diseased tissue sites across nearly 1,000 deceased individuals. [R27] So these are post-mortem tissues from deceased donors. On this release: The V10 release represents the final release to include new RNA sequencing data. As part of our QC, some samples from V8 have been removed and replaced in V10 with re-sequenced samples from the same tissue (where quality was improved). A number of tissue type swaps were also identified. [R25] A v8 figure, which is what the Human Protein Atlas folds into its own unit, and a v10 figure from this page are therefore two measurements and are never compared here.

The licence binds a redistributor in three ways [R24]: the acknowledgement sentence, printed in the provenance line with the day the data was obtained; not indicate or imply that the GTEx Portal has endorsed its products/services/applications. [R24], so the credit is a source line and never a badge; and maintain the most current version of all distributed data, or make known in a clear and conspicuous manner that the products/services/applications do not reflect the most current/accurate data available from the GTEx Portal. [R24], which is why the page carries the sentence: The figures shown may not reflect the most current data available from the GTEx Portal.

A gene high on this list is abundant in this tissue as GTEx measured it in post-mortem donors; whether it is a target worth knocking down is a question these numbers do not answer.

1. [R08] Lovén J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, et al. (2012). Revisiting global gene expression analysis. Cell 151:476-482. PMID 23101621, doi 10.1016/j.cell.2012.10.012.
2. [R24] GTEx Portal, Broad Institute of MIT and Harvard. GTEx Portal Data License. https://gtexportal.org/home/license, read 2026-09-09.
3. [R25] GTEx Portal, Broad Institute of MIT and Harvard. Frequently Asked Questions. https://gtexportal.org/home/faq, read 2026-09-09.
4. [R26] GTEx Portal, Broad Institute of MIT and Harvard. GTEx Portal API. https://gtexportal.org/api/v2/redoc, read 2026-09-09.
5. [R27] GTEx Portal, Broad Institute of MIT and Harvard. About Adult GTEx. https://gtexportal.org/home/aboutAdultGtex, read 2026-09-09.

This card is the atlas's own table joining its tissue names to GTEx's tissue sites, copied from its transcriptomics methods page, with the release's own sample count read beside each row; it is the only join between the two vocabularies this site offers, and it carries no expression value from either source.

The atlas states how it took GTEx in: The Genotype-Tissue Expression (GTEx) project collects and analyzes multiple human post mortem tissues. RNA-seq data from 36 of their tissue types was mapped based on RSEMv1.3.0 (v8) and the resulting TPM values have been included in the Human Protein Atlas for all corresponding genes that could be mapped from Gencode v26 to Ensembl version 109. [R29] So the atlas's GTEx column is GTEx v8, and this site's GTEx pages read v10: a value from each is two measurements of two sample sets, never compared and never used to check the other. The atlas's Retina row is not GTEx: The GTEx retina data are based on EyeGEx data from Ratnapriya et al., Nature Genetics 2019 and transcript abundance estimation was performed using Kallisto v0.48.0 using Ensembl version 109 as reference genome. [R29] That paper is [R09].

1. [R09] Ratnapriya R, Sosina OA, Starostik MR, Kwicklis M, Kapphahn RJ, Fritsche LG, et al. (2019). Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration. Nature Genetics 51:606-610. PMID 30742112, doi 10.1038/s41588-019-0351-9.
2. [R29] The Human Protein Atlas, proteinatlas.org. The human proteome, Methods summary, Transcriptomics. https://www.proteinatlas.org/humanproteome/tissue/method/transcriptomics, read 2026-09-09.