https://github.com/dhimmel/erc
Processing human Evolutionary Rate Covariation data
https://github.com/dhimmel/erc
data erc evolution evolutionary-rate-covariation genes hetionet human rephetio
Last synced: 11 months ago
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Processing human Evolutionary Rate Covariation data
- Host: GitHub
- URL: https://github.com/dhimmel/erc
- Owner: dhimmel
- Created: 2015-04-23T01:42:47.000Z (about 11 years ago)
- Default Branch: gh-pages
- Last Pushed: 2016-03-28T03:55:02.000Z (about 10 years ago)
- Last Synced: 2025-03-23T18:12:49.768Z (about 1 year ago)
- Topics: data, erc, evolution, evolutionary-rate-covariation, genes, hetionet, human, rephetio
- Language: Jupyter Notebook
- Homepage: https://doi.org/10.15363/thinklab.d57
- Size: 6.06 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 2
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Metadata Files:
- Readme: README.md
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README
# Processing human Evolutionary Rate Covariation data
This resource processes the [evolutionary rate covaration](http://csb.pitt.edu/erc_analysis/Methods.php) (ERC) data from [Priedigkeit et al 2015](https://doi.org/10.1371/journal.pgen.1004967 "Evolutionary Signatures amongst Disease Genes Permit Novel Methods for Gene Prioritization and Construction of Informative Gene-Based Networks"). ERC assesses whether two genes have a similar evolutionary history. See the corresponding [Thinklab discussion](http://doi.org/10.15363/thinklab.d57 "Selecting informative ERC (evolutionary rate covariation) values between genes") for more information.
## Files
`erc.ipynb` converts the raw ERC data into a tidy TSV (`erc_mam33.tsv.gz`) containing each gene pair mapped to Entrez Gene. `entrez-group.R` converts to using Entrez Gene as the primary gene identifiers. `erc_mam33-entrez.tsv.gz` is not tracked, since it's 821 MB, but the subset of gene pairs with ERC values >= 0.6 is stored in `erc_mam33-entrez-gt-0.6.tsv.gz`.
## License
All original content in this repository is licensed under [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/ "CC0 1.0 Universal: Public Domain Dedication"). ERC data is used with permission.