https://github.com/gersteinlab/brainpgene
https://github.com/gersteinlab/brainpgene
Last synced: 9 months ago
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- Host: GitHub
- URL: https://github.com/gersteinlab/brainpgene
- Owner: gersteinlab
- License: mit
- Created: 2025-08-18T22:26:17.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2025-08-18T22:58:36.000Z (10 months ago)
- Last Synced: 2025-08-19T00:25:28.707Z (10 months ago)
- Language: Jupyter Notebook
- Size: 53.7 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Comprehensive analysis of pseudogene expression in human and macaque brains compared to other tissues
## Overview
Pseudogenes are DNA sequences similar to protein-coding genes that contain disabling mutations rendering them unable to produce fully functional proteins. Traditionally, pseudogenes have been considered non-functional genomic elements that evolve under neutral selection, permitting the accumulation of deleterious mutations such as in-frame stop codons and frameshift insertions or deletions.
In this study, we aim to explore whether pseudogenes could possess putative biological relevance in the brain. To that end, we propose three primary objectives:
- characterizing the tissue- and brain region-specificity of pseudogene expression;
- identifying temporally dynamic pseudogenes across diverse brain regions;
- identifying differentially expressed pseudogenes associated with psychiatric disorders.
## Dataset
**PsychENCODE Consortium (PEC)**
- [Spatiotemporal transcriptomic divergence across human and macaque brain development](https://www.science.org/doi/10.1126/science.aat8077) (Zhu et al., *Science*, 2018).
- [Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder](https://www.science.org/doi/10.1126/science.aat8127) (Gandal et al., *Science*, 2018)
**ENCODE EN-TEx**
- [The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models](https://www.cell.com/cell/fulltext/S0092-8674(23)00161-7) (Rozowsky et al., *Cell*, 2023)
The publicly available RNA-seq reads used in this study were downloaded as BAM files from [Synapse](https://www.synapse.org/).
The expression data of the pseudogenes and protein-coding genes in human and macaque quantified based on the computational framework in this study were deposited to [Zenodo](https://doi.org/10.5281/zenodo.16810204).
## For more information
If you have additional questions, please contact [Yunzhe Jiang](mailto:yunzhe.jiang@yale.edu) and [Yucheng T. Yang](mailto:yangyc2016@gmail.com).