This repository hosts supplementary materials for the manuscript:
Time‑Evolving SASP Gene‑Set Ensemble Identifies IGFBP7 and CDKN1A as a Marker Pair for Senescent Fibroblast Subpopulations Across Tissues
It includes the figure depicting SASP heterogeneity in WI‑38 fibroblasts and per‑tissue differential expression results (senescent/stressed vs. control fibroblasts) derived from our ensemble-of-gene-sets (EGS) SASP scoring workflow.
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├─ png/
│ └─ supplementary_fig_s2.png
├─ tsv/
│ ├─ disco_eye_fibroblasts_tissue_ctrl_vs_senescent_fibroblasts.tsv
│ ├─ disco_fibroblasts_lung_tissue_ctrl_vs_senescent_fibroblasts.tsv
│ └─ disco_skin_fibroblasts_tissue_ctrl_vs_senescent_fibroblasts.tsv
└─ README.md
The figure below summarizes SASP gene expression heterogeneity across WI‑38 population doubling levels (PDLs), highlighting subpopulation‑ and time‑dependent SASP programs.
What to look for:
- Many canonical SASP genes are not uniformly expressed; instead they are enriched in specific subpopulations.
- Patterns differ between early vs. mature senescence, consistent with temporal (time‑evolving) heterogeneity.
Below are per‑tissue differential expression (DE) outputs comparing control vs. senescent/stressed fibroblasts selected by SASP scores/EGS. Each TSV typically contains: gene, logFC/avg_log2FC, p_val, p_val_adj/FDR, and may include detection rates/mean expression columns depending on your pipeline.
- File:
tsv/disco_fibroblasts_lung_tissue_ctrl_vs_senescent_fibroblasts.tsv - Description: Differential expression between predicted control and senescent/stressed lung fibroblasts. Useful for validating cross‑tissue markers (e.g., IGFBP7, CDKN1A) and comparing with WI‑38 signatures.
- File:
tsv/disco_skin_fibroblasts_tissue_ctrl_vs_senescent_fibroblasts.tsv - Description: Differential expression between predicted control and senescent/stressed skin fibroblasts. Highlights tissue‑type heterogeneity (e.g., IGFBP6 elevation in skin) relative to WI‑38.
- File:
tsv/disco_eye_fibroblasts_tissue_ctrl_vs_senescent_fibroblasts.tsv - Description: Differential expression between predicted control and senescent/stressed eye fibroblasts.
🧪 Interpretation Notes
SASP scores/EGS leverage an ensemble of up/down gene sets to better capture SASP heterogeneity (subpopulation‑ and time‑dependent signals), helping reduce false positives relative to single‑module scores. Cross‑tissue results often identify IGFBP7 (with CDKN1A/p21) as a robust senescence‑associated signature; other SASP factors can be tissue‑dependent and heterogeneous.
We welcome questions, feedback, and scientific discussion related to the SASP-score project, senescence biology, and the ensemble-of-gene-sets (EGS) framework.
There are several ways to communicate or contribute:
Use Discussions for:
- Questions about the method or data
- Scientific discussion about SASP heterogeneity
- Suggestions for improvements or new analyses
- Sharing related ideas, feedback, or examples
👉 Start a Discussion:
https://github.com/hyunsoo77/SASP_score/discussions
Use Issues for:
- Reporting problems with files or links
- Requesting clarification about datasets
- Bug reports or reproducibility issues
- Feature requests related to the repository
👉 Open an Issue:
https://github.com/hyunsoo77/SASP_score/issues
For private correspondence related to collaborations or scientific inquiries:
Email: kimx0662@umn.edu
We encourage open scientific dialogue and collaboration.
Thank you for your interest in the SASP-score project!
✉️ Questions & Discussion Please open an Issue or Discussion in this repository with:
A clear description of the question Relevant figures or code snippets The exact TSV/section you are referring to
We welcome feedback from the community.
📜 Citation If you use these materials, please cite the manuscript (update when available):
Authors. Time‑Evolving SASP Gene‑Set Ensemble Identifies IGFBP7 and CDKN1A as a Marker Pair for Senescent Fibroblast Subpopulations Across Tissues. Journal, Year. DOI