Protocol for reconstructing spatially aware receptor-TF-target signaling cascades using spatial transcriptomics
Yao Li, Xiaobin Liu, Xinkai Yan, Guangyi Fan, Mengyang Xu · 2025
Read Protocol for reconstructing spatially aware receptor-TF-target signaling cascades using spatial transcriptomics by Yao Li, Xiaobin Liu, Xinkai Yan, Guangyi Fan, Mengyang Xu (2025) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-12756632.txt.
Description
Yao Li and four co-authors lay out a step-by-step protocol in a 2025 paper for tracing cell signaling in space. Spatial transcriptomics reads which genes are on, spot by spot, across a tissue slice. Older network-building methods ignore where those spots sit, losing the geography of the signals.
Their method, called SpaGRN, rebuilds chains that run from a surface receptor through a transcription factor to its target genes, with the tissue map built in. The protocol walks through data cleaning, spatial pattern checks, co-activity mapping, and motif hunting, ending in three-dimensional views. It suits tangled tissues like growing embryos and tumors, where place shapes the message.
Catalog record
| CREATOR | Yao Li, Xiaobin Liu, Xinkai Yan, Guangyi Fan, Mengyang Xu |
|---|---|
| YEAR | 2025 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 82 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |