Cell type enrichment analysis with xCell

MS Maria-Fernanda Senosain
YZ Yong Zou
TN Tatiana Novitskaya
GV Georgii Vasiukov
AB Aneri B. Balar
DR Dianna J. Rowe
DD Deon B. Doxie
JL Jonathan M. Lehman
RE Rosana Eisenberg
FM Fabien Maldonado
AZ Andries Zijlstra
SN Sergey V. Novitskiy
JI Jonathan M. Irish
PM Pierre P. Massion
request Request a Protocol
ask Ask a question
Favorite

Using TCGA data, we selected patients with disease stage between I and III. After applying log transformation (log2(FPKM+1)) we computed the quantiles of expression of MHC-II related genes. Patients were labeled as “low” if the expression of the gene in question was below the first quantile (25%) and “high” if it was higher than the third quantile (75%). Cell type enrichment analysis results for TCGA data were downloaded from the xCell website (https://xcell.ucsf.edu/) and patient groups were compared.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A