Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Method

Data download and processing

Screening of differentially expressed genes

GO enrichment analysis and KEGG pathway analysis

Gene co-expression network analysis

Hub gene screening

Data set verification

Hub gene survival analysis

Results

Acquisition of microarray data

DEGs screening

GO enrichment analysis and KEGG pathway analysis results

Gene co-expression network analysis results

Screening of hub genes

Survival analysis of hub genes

Data set verification

Survival analysis

Discussion

Conclusions

Supplemental Information

Difference analysis of 34 normal and 269 CRC samples was performed and obtained 1,216 DEGs.

DOI: 10.7717/peerj.9633/supp-1

GO enrichment analysis result.

DOI: 10.7717/peerj.9633/supp-2

KEGG enrichment analysis result.

DOI: 10.7717/peerj.9633/supp-3

Train set dataset.

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Test set dataset.

(A) Gene enrichment analysis results of the intersection region of DEGs and yellow modules. (B) Gene enrichment analysis results of the intersection region of DEGs and black modules (C) Gene enrichment analysis results of the intersection region of DEGs and blue modules. (D) Yellow module GO enrichment analysis results. (E) Black module GO enrichment analysis results. (F) Blue Yellow module GO enrichment analysis results.

DOI: 10.7717/peerj.9633/supp-5

The clinical information related to GSE26712.

DOI: 10.7717/peerj.9633/supp-6

The results of gene enrichment analysis of the intersection of DEGs and yellow, black and blue modules.

DOI: 10.7717/peerj.9633/supp-7

The degree of each node in the network based on Cytoscope.

DOI: 10.7717/peerj.9633/supp-8

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Jie Meng conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Rui Su performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Yun Liao analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, contributed to cell lines and some consumables, and approved the final draft.

Yanyan Li analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Ling Li conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw measurements are available in the Supplemental Files.

Funding

The authors received no funding for this work.

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