https://github.com/dhimmel/hgnc
Extracting human gene families from HGNC
https://github.com/dhimmel/hgnc
data gene-families genes hgnc hugo human
Last synced: about 2 months ago
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Extracting human gene families from HGNC
- Host: GitHub
- URL: https://github.com/dhimmel/hgnc
- Owner: dhimmel
- License: cc0-1.0
- Created: 2017-01-25T18:05:54.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-01-26T19:38:34.000Z (over 9 years ago)
- Last Synced: 2025-03-23T18:12:45.217Z (over 1 year ago)
- Topics: data, gene-families, genes, hgnc, hugo, human
- Language: Jupyter Notebook
- Homepage: https://thinklab.com/d/34#13
- Size: 3.67 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# Extracting human gene families from HGNC
This repository processes the [gene family data](https://doi.org/10.1186/s40246-016-0062-6 "Gray et al (2016) A review of the new HGNC gene family resource. Human Genomics") from HGNC. In the future, the repository may expand its scope to process other types of HGNC data.
## Notebooks
+ [`1.download.ipynb`](1.download.ipynb) downloads HGNC data. Check this notebook to see the last modified dates of downloaded files.
+ [`2.families.ipynb`](2.families.ipynb) constructs the gene family ontology in `networkx`. Annotates gene families with their corresponding Entrez Gene IDs. Gene membership in a family is propagated, e.g. genes belonging to the "[Glutamate metabotropic receptors](http://www.genenames.org/cgi-bin/genefamilies/set/281)" family also belong to the "Glutamate receptors" family.
## Files & Directories
+ [`download`](download) contains unmodified downloads from the EBI FTP site.
+ [`data`](data) contains generated datasets. [`families.graphml`](data/families.graphml) contains a GraphML-formatted network of the HGNC gene family ontology. [`gene-families.tsv`](data/gene-families.tsv) contains the mapping between gene families and Entrez genes.
## Questions
Have a question? Submit all feedback or questions via [GitHub issues](https://github.com/dhimmel/hgnc/issues)!