Network-based identification of biomarkers for colon adenocarcinoma

BMC Cancer
Fuyan HuXiaoping Liu

Abstract

As one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges. We firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively. Classification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they...Continue Reading

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Datasets Mentioned

BETA
GSE21510
GSE39582

Methods Mentioned

BETA
surgical resection
GTPase
Nucleotide Exchange

Software Mentioned

STRING
R package ‘ clusterProfiler ’
DAVID
ConsensusClusterPlus R - package
COAD
kernlab
LASSO
maftools
ROCR
Bioconductor maftools

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