https://github.com/dhimmel/bgee

Extracting anatomy-specific gene expression in humans from Bgee
https://github.com/dhimmel/bgee

anatomy bgee gene gene-expression hetionet rephetio transcriptomics tsv

Last synced: 22 days ago
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Extracting anatomy-specific gene expression in humans from Bgee

• Host: GitHub
• URL: https://github.com/dhimmel/bgee
• Owner: dhimmel
• Created: 2015-06-19T20:59:12.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2016-03-08T01:54:17.000Z (almost 9 years ago)
• Last Synced: 2024-10-15T15:09:05.168Z (2 months ago)
• Topics: anatomy, bgee, gene, gene-expression, hetionet, rephetio, transcriptomics, tsv
• Language: Jupyter Notebook
• Homepage: http://doi.org/10.15363/thinklab.d124
• Size: 2.69 MB
• Stars: 2
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Extracting anatomy-specific gene expression in humans from Bgee

[![DOI: 10.5281/zenodo.47157](https://zenodo.org/badge/doi/10.5281/zenodo.47157.svg)](https://doi.org/10.5281/zenodo.47157)

[Bgee](http://bgee.org/) is a database that integrates gene expression data from both microarray and RNA-seq experiments. The Bgee curators annotate samples by their species, anatomical structure, and developmental stage. Bgee leverages anatomical and developmental ontologies to call whether a gene is present or absent and under/over-expressed in a given condition.

Here, we process Bgee to generate gene expression profiles for human anatomical structures (tissues). We extract two gene expression measures:

+ gene presence — whether a gene is expressed or not in a given anatomy for adult humans. See the results at [`data/present-in-adult.tsv.gz`](data/present-in-adult.tsv.gz).

+ differential expression — whether a gene is under or over-expressed in a given anatomy for post-juvenile adults. See the results at [`data/diffex.tsv.gz`](data/diffex.tsv.gz).

See our _Thinklab_ [project](http://doi.org/10.15363/thinklab.40 "Repurposing drugs on a hetnet") and [discussion on processing Bgee](http://doi.org/10.15363/thinklab.d124 "Processing Bgee for tissue-specific gene presence and over/under-expression") for additional context.

## Execution

Execute [`download.sh`](download/download.sh) from the `download` directory to retrieve the raw Bgee downloads.

Then the notebooks are executed in the following order:

1. [`developmental-stages.ipynb`](developmental-stages.ipynb) — extract a table of developmental stages ([`data/stages.tsv`](data/stages.tsv)). This table is used to filter for adult stages.

2. [`bgee.ipynb`](bgee.ipynb) — process raw Bgee data and extract gene presence and differential expression datasets.

## License

All original content in this repository is released under [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/ "Creative Commons · Public Domain Dedication"). Please refer to [Bgee](http://bgee.org/) for the licensing and reuse of their data.