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Published on: July 22, 2020
Bioinformatics analysis of RNA-seq data revealed critical genes in colon adenocarcinoma
1Department of Gastroenterology, The Third People's Hospital of Chengdu, The Second Affiliated Chengdu Clinical College of Chongqing Medical University, Chengdu, Sichuan, China. zhangtttd@aliyun.com.
Objective:
RNA-seq data of colon adenocarcinoma (COAD) were analyzed with bioinformatics tools to discover critical genes in the disease. Relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated.
Materials And Methods:
RNA-seq data of COAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. False positive discovery (FDR) < 0.05 and |log2 (fold change)|>1 were set as the cut-offs to screen out differentially expressed genes (DEGs). Gene coexpression network was constructed with package Ebcoexpress. GO enrichment analysis was performed for the DEGs in the gene coexpression network with DAVID. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was also performed for the genes with KOBASS 2.0. Modules were identified with MCODE of Cytoscape. Relevant small molecules drugs were predicted by Connectivity map. Relevant miRNAs and TFs were searched by WebGestalt.
Results:
A total of 457 DEGs, including 255 up-regulated and 202 down-regulated genes, were identified from 437 COAD and 39 control samples. A gene coexpression network was constructed containing 40 DEGs and 101 edges. The genes were mainly associated with collagen fibril organization, extracellular matrix organization and translation. Two modules were identified from the gene coexpression network, which were implicated in muscle contraction and extracellular matrix organization, respectively. Several critical genes were disclosed, such as MYH11, COL5A2 and ribosomal proteins. Nine relevant small molecule drugs were identified, such as scriptaid and STOCK1N-35874. Accordingly, a total of 17 TFs and 10 miRNAs related to COAD were acquired, such as ETS2, NFAT, AP4, miR-124A, MiR-9, miR-96 and let-7.
Conclusions:
Several critical genes and relevant drugs, TFs and miRNAs were revealed in COAD. These findings could advance the understanding of the disease and benefit therapy development.
Insights
Bioinformatics analysis of colon adenocarcinoma (COAD) identified critical genes, including MYH11 and COL5A2. This study also revealed potential therapeutic targets like scriptaid and specific microRNAs (miRNAs) for COAD treatment.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Colon adenocarcinoma (COAD) is a significant health concern.
- Understanding the molecular mechanisms underlying COAD is crucial for developing effective treatments.
Purpose of the Study:
- To identify critical genes involved in COAD using bioinformatics analysis.
- To investigate potential therapeutic targets, including small molecule drugs, transcription factors (TFs), and microRNAs (miRNAs), for COAD.
Main Methods:
- RNA-sequencing data from The Cancer Genome Atlas (TCGA) for COAD were analyzed.
- Differential gene expression analysis, gene coexpression network construction, and enrichment analyses (GO, KEGG) were performed.
- Identification of key genes, modules, small molecules, TFs, and miRNAs using bioinformatics tools.
Main Results:
- 457 differentially expressed genes (DEGs) were identified in COAD samples compared to controls.
- Key genes such as MYH11, COL5A2, and ribosomal proteins were highlighted.
- Nine small molecule drugs, 17 TFs, and 10 miRNAs were identified as potentially relevant to COAD.
Conclusions:
- This study reveals critical genes, drugs, TFs, and miRNAs associated with COAD.
- The findings contribute to a better understanding of COAD and may aid in developing new therapeutic strategies.
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