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. 2018 Jul;16(1):48-54.
doi: 10.3892/ol.2018.8668. Epub 2018 May 8.

Transcriptome profiling analysis reveals biomarkers in colon cancer samples of various differentiation

Tonghu Yu  1 , Huaping Zhang  1 , Hong Qi  2
Affiliations

Transcriptome profiling analysis reveals biomarkers in colon cancer samples of various differentiation

Tonghu Yu et al. Oncol Lett. 2018 Jul.

Abstract

The aim of the present study was to investigate more colon cancer-related genes in different stages. Gene expression profile E-GEOD-62932 was extracted for differentially expressed gene (DEG) screening. Series test of cluster analysis was used to obtain significant trending models. Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, functional and pathway enrichment analysis were processed and a pathway relation network was constructed. Gene co-expression network and gene signal network were constructed for common DEGs. The DEGs with the same trend were clustered and in total, 16 clusters with statistical significance were obtained. The screened DEGs were enriched into small molecule metabolic process and metabolic pathways. The pathway relation network was constructed with 57 nodes. A total of 328 common DEGs were obtained. Gene signal network was constructed with 71 nodes. Gene co-expression network was constructed with 161 nodes and 211 edges. ABCD3, CPT2, AGL and JAM2 are potential biomarkers for the diagnosis of colon cancer.

Keywords: biomarker; colon cancer; different stage; differently expressed genes.

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Figures

Figure 1.
Figure 1.
Cluster of the screened differentially expressed genes. The red profiles are statistically significant, but the blue profiles have no statistical significance.
Figure 2.
Figure 2.
Pathway relation network of pathways enriched by differentially expressed genes. The nodes and edges are pathways and their regulation and relationships, respectively.
Figure 3.
Figure 3.
Gene signal network of common differentially expressed genes (DEGs). The nodes and edges are common DEGs and their regulation and relationships, respectively.
Figure 4.
Figure 4.
Gene co-expression network of common differentially expressed genes (DEGs). The nodes and edges are common DEGs and their regulation and relationships, respectively. The solid lines show the positive correlation while the dashed lines show the negative correlation.
See this image and copyright information in PMC

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