Circular RNA Signatures Of Human Healing And Non-Healing Wounds
If you use it in published research, please cite: Maria A. Toma*, Zhuang Liu*†, Qizhang Wang, Letian Zhang, Dongqing Li, Pehr Sommar, Ning Xu Landén†. Circular RNA signatures of human healing and non-healing wounds. Journal of Investigative Dermatology (*Co-first author, †Co-senior author). https://doi.org/10.1016/j.jid.2022.03.024
In this tutorial, we will give you a brief introduction of playing around with the circRNA signatures visualization tool for normal acute wounds and venous ulcers in human skin.
There are three sections as below:
- circRNA expression
- DE circRNA analysis
- cirRNA-mRNA WGCNA
- circRNA expression: You can check the expression of circular RNA by searching our custom names (Most of them are same as documented in circAtlas 2.0 database, e.g. HSA-TNFRSF21_0001), as well as universal circRNA names from different circRNA databases (e.g. circBase: hsa_circ_0001610, CIRCpedia v2: HSA_CIRCpedia_55208), or even the coordinates (e.g. chr6:47283938|47286595). Saving these plots as .PDF files.
- DE circRNA analysis: Here, checking the lists of circRNAs in the differential expression (DE) analysis across different conditions (e.g. VU vs. Skin, VU vs. Wound1, VU vs. Wound7) by using different criteria (e.g. log2(fold change), p adjust value). Saving the heatmap and dataset if you like it.
- cirRNA-mRNA WGCNA: In addition, checking the gene list of circRNA-mRNA co-expressed module in the weighted gene co-expression network analysis (WGCNA) in different conditions. Visualizing the lists of genes and gene ontology (GO) terms for each module. Saving the dataset if you like it.