https://github.com/linas/biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes
https://github.com/linas/biome-distribution

genomic-data-analysis genomics-visualization proteogenomics proteomics reactome reactome-pathway

Last synced: 5 months ago
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Research into statistical distributions of genomes, proteomes and reactomes

• Host: GitHub
• URL: https://github.com/linas/biome-distribution
• Owner: linas
• License: other
• Created: 2020-01-23T21:16:36.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2022-02-14T20:19:41.000Z (over 4 years ago)
• Last Synced: 2025-01-22T22:29:11.424Z (over 1 year ago)
• Topics: genomic-data-analysis, genomics-visualization, proteogenomics, proteomics, reactome, reactome-pathway
• Language: Scheme
• Size: 14.2 MB
• Stars: 6
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

Awesome Lists containing this project

README

          

Biome Distributions

-------------------

Research concerning the statistical distribution of genetic

interactions, the proteins expressed by genes, and their

participation in reaction pathways.

The primary result is a paper, being prepared for publication.

It is in the [paper](./paper) directory. The

[PDF is here](./paper/biome-distributions.pdf).

It was naively hypothesized that genome/proteome reaction pathways

form a scale-free network, and thus would have a Zipfian distribution.

Much to our surprise, this is not the case! It seems like *everything*

follows a square-root Zipfian distribution! I do not know of any

network theory or biology theory that would explain this, so it is

a surprise.

An exploration of the mutual information of interaction pathways is

also performed. It appears that these are easily fit with a bimodal

Gaussian distribution.

This is for human genome/reactome data. I don't doubt that the results

are generic in biology.

### Directory layout

Other directories here:

* [diary](./diary) A research diary of notes.

* [graphs](./graphs) Graphs and the tools used to prepare them.

* [src](./src) Source code for loading, processing and analyzing

  the genomic and proteomic data, including reactome data, etc.

### License


This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.