Gene-Regulatory Networks (GRNs) | 进阶分析

单细胞RNA数据怎么玩，不做这个fancy的分析就太out了，必须做，且必须扯。

 

先看看别人怎么玩的：

对应section：Activation of Unique Gene-Regulatory Networks (GRNs) Underlies Regenerative Competence in Wound- Responsive Fibroblasts【对应Figure 5】

 

To identify signaling networks that might confer regenerative or fibrotic fibroblast function, we first performed single-cell regulatory network inference and clustering (SCENIC) analysis (Aibar et al., 2017) on Hic1-lineage fibroblasts from LWs, SWs, and uninjured skin (Figures S5A–5E).【那我们则可以】

To dissect WIHN regulators active in a region-specific fashion, we performed t-SNE reduction using SCENIC’s regulon matrix and annotated fibroblasts based on their location in LWs 14 dpw (LWC or LWP; Figures 5A–5C).

Although transcription factors (TFs) such as Cd59 and Prxx1 exhibited predictable patterns of transcript enrichment (yellow) paired with concomitant activation of downstream regulatory networks (blue) in LWP fibroblasts (Figure 5B), we observed highly discrepant TF network activity in LWC fibroblasts (Figure 5C).

Notably, although LWC and LWP fibroblasts expressed comparable levels of Thap11, Gt3a, and Rara mRNA, this was not reflected by TF network activity because they were preferentially active (area under the curve [AUC]; Figures 5B and 5C) within LWC fibroblasts.

 

 

怎么展示结果：

core regulons

regulon (co-expressed target genes regulated by a transcription factor)【定义清晰】

 

 

 

参考：

Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing - CSC - 2020

https://ars.els-cdn.com/content/image/1-s2.0-S1934590920303465-mmc1.pdf - CSC - Figure Sx

 

工具：

A scalable SCENIC workflow for single-cell gene regulatory network analysis - nature protocols - 2020【新版，For a data set of 10,000 genes and 50,000 cells, the pipeline runs in <2 h.】

aertslab/SCENICprotocol - GitHub