TF IDR Paper

Code to reproduce analyses and figures for the preprint:

Disordered but Different: The Unique Characteristics of Intrinsically Disordered Regions in Human Transcription Factors
Susie Song and Joshua Akey
Preprint: bioRxiv (2026) https://doi.org/10.64898/2026.01.27.700206

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What this repository contains

This repository contains scripts and workflows to:

• annotate intrinsically disordered regions (IDRs) across the human proteome
• map protein-level annotations to genomic coordinates
• integrate population variation (e.g., gnomAD) with IDR vs non-IDR intervals
• run downstream statistics and generate all manuscript figures

Repository layout

.
├── data/                 # input datasets (sources in Data Availability) 
├── envs/                 # conda env files / requirements
├── figures/              # all main and supplemental figures 
├── notebooks/            # Jupyter notebooks to generate all analysis & figures
├── results/              # generated intermediate outputs 
├── scripts/              # one-off analysis scripts
├── src/                  # reusable modules
└── README.md

Getting Started

Requirements

Install dependencies:

pip install -r envs/requirements.txt

Data Availability

Large data files are not included in this repository. Below are instructions to download required resources.

Required inputs

Input	Download	Description	Source	Version	Format	Example path
Proteome FASTA	Link	Human proteome sequences	UniProt	UP000005640 (2025_04)	.fasta	data/raw/uniprot/UP000005640_9606.fasta
UniProt ID mappings	Link	Reference genome build	GENCODE	GRCh38.p14	.fa	data/proteome_annot/uniprot/UP000005640_9606.idmapping
TF list	Link	Human TF catalog	Lambert et al.	2018	.csv	data/proteome_annot/tfs/DatabaseExtract_v_1.01.csv
GenOrigin	Link	Gene age catalog	GenOrigin	2021	.csv	data/gene_age/genorigin/Homo_sapiens.csv
GenEra	Link	Gene age catalog	GenEra	-	.tsv	data/gene_age/genera/Homo_sapiens_gene_ages.tsv
PhyloP	Link	-	-	-	``	``
GO Association	Link	-	-	2025_07_22	``	``
GO OBO	Link	-	-	-	``	``
STRING	Link	PPI	STRING	v12.0	``	``
GRNDB	Link	-	-	-	``	``
Human Protein Atlas	Link	HPA	HPA	v25.0	``	``
GTEx Fine-mapped QTLs	Link	GTEx Portal	GTEx	v10 (2024_11)	``	``
Translational efficiency	Link	Supplementary Table 1	Zheng et al.	2025	``	``
gnomAD	Link	Population variant sites	gnomAD	v4.1 exomes	``	``
1KGP	Link	-	-	-	``	``
Lethal OMIM	Link	Lethal Phenotypes Portal	Lethal Phenotypes Portal	(2024_11)	``	``
HGMD	Link	Disease Variants	HGMD	Professional	``	``

Citation

If you use this repository, cite the following:

BibTeX

@article{song_akey_2026_disordered_but_different,
  title   = {Disordered but Different: The Unique Characteristics of Intrinsically Disordered Regions in Human Transcription Factors},
  author  = {Song, Susie and Akey, Joshua},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.01.27.700206},
  url     = {https://doi.org/10.64898/2026.01.27.700206}
}