Compilation of human secretome-encoding genes, their phylogenetic age, and some of their expression properties.
Data files
May 06, 2026 version files 138.85 KB
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Dataset_EV1.csv
135.58 KB
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README.md
3.28 KB
Abstract
This dataset is a compilation of human secretome-encoding genes, their phylogenetic age, and some of their expression properties. This information was used to determine whether all secretome-by-evolutionary-transition combinations experienced similar gains of new genes during vertebrate evolution. We found that the male reproductive secretome experienced the largest addition of new genes during the eutherian radiation compared to any other secretome-by-evolutionary-transition combination. Most of these new genes are preferentially expressed in the epididymis, pointing to this organ as the one that underwent the largest reconfiguration among those in the male reproductive tract. These data can be used with no restrictions.
Dataset DOI: 10.5061/dryad.pvmcvdp0s
Description of the data and file structure
The data in the file Dataset_EV1.csv were obtained from the most comprehensively characterized collection of secretomes in humans at the molecular level (Uhlen et al. 2019; DOI: 10.1126/scisignal.aaz027). The human secretome comprises 2,520 genes encoding predicted secretory proteins based on subcellular location, presence of signal peptides, and absence of transmembrane domains. These secreted proteins are categorized into nine distinct secretomes based on where they are produced in the human body: blood, brain, digestive system, female reproductive (FR) system, male reproductive (MR) system, immunoglobulins, intracellular and membrane (as a control), extracellular matrix, and other tissues. An additional category of unknown location was also retrieved. This information was obtained from the Human Protein Atlas v24.0 (https://www.proteinatlas.org/humanproteome/tissue/secretome). Expression profiles and expression-level based categorization of genes across tissues was obtained from the same database, and the expression breadth value (i.e., the tau index value) was taken as reported (Palmer et al. 202; DOI: 10.18632/aging.202648). Not all the genes have information for expression-level based categorization and the tau index, in which case the cell is empty. Further, the evolutionary origin of 19,665 protein-coding human genes across the vertebrate phylogeny, distinguishing seven evolutionary branches that correspond to key evolutionary transitions, was taken as reported (Chen et al. 2025; DOI: 10.1101/2023.11.14.567139).
Files and variables
File: Dataset_EV1.csv
Description:
Variables
- Gene Name
- Ensembl ID (From the hg38_ver95 release)
- Gene Age (Branch of origin within the vertebrate phylogeny according to Chen et al. (2025): euteleostomi and older (br0), tetrapoda (br1), amniota (br2), mammalia (br3), theria (br4), eutheria (br5), and primate (br6)).
- Secretome (According to Uhlen et al. (2019)).
- Expression Pattern Across Male Reproductive Tissues (1, expressed; 0, nonexpressed. Testis_Epididymis_Prostate_Seminal VesicleTestis_Epididymis_Prostate_Seminal Vesicle)
- Tissue-Enriched (1, tissue-enriched -at least four-fold higher expression in a given tissue compared to any other body tissue-; 0, non-tissue-enriched).
- Tau Index (According to Palmer et al. (2021)).
Code/software
Google Sheets
Access information
Other publicly accessible locations of the data:
- N/A
Data was derived from the following sources:
- Secretome data, including expression profiles (Uhlen et al. 2019; DOI: 10.1126/scisignal.aaz0274).
- Phylogenetic age of genes (Chen et al. 2025; DOI: 10.1101/2023.11.14.567139).
- Tau index values (Palmer et al. 202; DOI: 10.18632/aging.202648).
Secretome-encoding genes were retrieved from the Human Proteome Atlas (https://www.proteinatlas.org/) and matched with different age classes as reported by Chen et al. 2025 (Chen et al. 2025; DOI: 10.1101/2023.11.14.567139).