Computational codes for identification of master regulators of high-risk nasopharyngeal carcinoma
Creators
- 1. State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China.
- 2. 1. State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China. 2. Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510060, P.R. China.
Description
The Algorithm for the Reconstruction of Accurate Cellular Networks through Adaptive Partitioning (ARACNe-AP) was applied to construct transcriptional interactomes in gene expression profiles from cohorts of patients with nasopharyngeal carcinoma. Then the Virtual Inference of Protein Activity by Enriched Regulon (VIPER) algorithm was applied to prioritize master regulator proteins based on the inferred transcriptional activity.
Scripts:
· 1-ARACNe-AP.ps1: PowerShell script for the construct of transcriptional interactomes.
· 2-VIPER.R: R script for the identification of master regulator proteins based on the inferred transcriptional activity.
Data:
· Expression matrix (GSE12452 and GSE102349): Public nasopharyngeal carcinoma datasets, which can be obtained from GEO database (https://www.ncbi.nlm.nih.gov/geo/).
· Transcription Factors (TFs) list: List of Human transcription factors, which can be obtained from http://humantfs.ccbr.utoronto.ca/download/v_1.01/TF_names_v_1.01.txt
Please refer to the following paper for more details:
Ya-Qin Wang#, Dong-Hong Wu#, Denghui Wei#, Jia-Yi Shen#, Zi-Wei Huang#, et al., Jiawei Lv*, Yu-Pei Chen*. TEAD4 is a master regulator of high-risk nasopharyngeal carcinoma.
Files
Scripts.zip
Files
(3.0 kB)
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