Published May 4, 2025 | Version v1
Dataset Open

Isoswitching drives the aging process in human brains - Data and models

Authors/Creators

  • 1. EDMO icon Johns Hopkins University

Description

Contents

input_files
Contains all transcript quantification results and associated sample metadata for the datasets analyzed in this study. Also includes the list of the top 1,000 most predictive genes identified by the model in the file _imp_genes.txt.

SPIT_analysis
Results from DTU analysis comparing prenatal and postnatal LIBD brain samples.

model_source.ipynb
Main analysis notebook for isoform trajectories and brain age prediction models using LIBD data. Also includes validation on the Cardoso-Moreira brain dataset and GTEx heart samples.

Software requirements:

numpy>=1.21.0
pandas>=1.3.0
scipy>=1.7.0
matplotlib>=3.4.0
seaborn>=0.11.0
scikit-learn>=0.24.0

Run time: ~ 1 hr

coverage
.bigwig files showing stage-specific read coverage. These can be visualized in IGV.

func_analysis
Protein-level comparison of isoform pairs from 1,000 predictive genes. Contains:
Pairwise alignments
Isoform-specific coordinates
Structural domain annotations via Foldseek (CATH50)
func_analysis_table.tsv with top domain hits for 134 isoform-specific sequences

Files

base_analysis.zip

Files (17.6 GB)

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md5:1c07724d19e919e95a502b47727b4996
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Additional details

Dates

Submitted
2025-05-04

References

  • Collado-Torres, L. et al. Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia. Neuron 103, 203-216.e208 (2019). https://doi.org:https://doi.org/10.1016/j.neuron.2019.05.013
  • Jaffe, A. E. et al. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nature Neuroscience 18, 154-161 (2015). https://doi.org:10.1038/nn.3898
  • Cardoso-Moreira, M. et al. Gene expression across mammalian organ development. Nature 571, 505-509 (2019). https://doi.org:10.1038/s41586-019-1338-5
  • Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nature Genetics 45, 580-585 (2013). https://doi.org:10.1038/ng.2653