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Analysis of differential expression in tumor and matched normal tissues

YY Ying Yuan

Last updated date: Jul 1, 2023 Views: 743 Forks: 0

original An abbreviated version of this protocol was published in Chinese Journal of Cancer Research in Feb, 2021
Pan-cancer analyses demonstrate that ANKRD6 is associated with a poor prognosis and correlates with M2 macrophage infiltration in colon cancer
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1、Expression anlysis

1.1、ANKRD6 expression in cancers was analyzed with the Oncomine database (https://www.oncomine.org/resource/login.html)

1.2、The differential expression of ANKRD6 mRNA between tumor and normal tissues was analyzed by TIMER (TCGA gene expression RNA-seq data)

1.3、The differential expression of ANKRD6 mRNA between tumor and normal tissues was analyzed by GEPIA.

 

2、Prognosis anlysis

2.1、Based on the Affymetrix microarray, we used PrognoScan technology to study the relationship between ANKRD6 expression and the prognosis of different cancers.

2.2、TCGA-RNA sequencing data were also used to analyze the prognostic potential of ANKRD6 in different cancers by GEPIA

 

3、Immune infiltration anlysis

3.1、Using TIMER, we investigated the correlations between ANKRD6 expression and immune infiltration levels.

3.2、Using the CIBERSORT algorithm, we evaluated the abundance of TILs in the colon microenvironment using the TCGA gene expression data

3.3、We used IHC to analysis the correlation between different ANKRD6 expression levels and OS and M2 macrophages in colon cancer（CD68, CD163 and ANKRD6）

Copyright: © 2023 The Author(s); This is an open-access article under the CC BY-NC license (https://creativecommons.org/licenses/by-nc/4.0/).
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Yuan, Y(2023). Analysis of differential expression in tumor and matched normal tissues. Bio-protocol Preprint. bio-protocol.org/prep2358.
  2. Bai, R., Wu, D., Shi, Z., Hu, W., Li, J., Chen, Y., Ge, W., Yuan, Y. and Zheng, S.(2021). Pan-cancer analyses demonstrate that ANKRD6 is associated with a poor prognosis and correlates with M2 macrophage infiltration in colon cancer. Chinese Journal of Cancer Research 33(1). DOI: 10.21147/j.issn.1000-9604.2021.01.10

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