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Identification of differentially expressed genes and their upstream regulators in colorectal cancer
Abstract:
To identify the differentially expressed genes (DEGs) and their transcription factors (TFs) in colorectal cancer (CRC). We performed an integrated analysis of microarray studies. Functional annotation and CRC-specific transcriptional regulatory network construction were performed. Expression of selected DEGs and TFs was verified with The Cancer Genome Atlas (TCGA) data sets and qRT-PCR. SurvMicro was used to analyze the correlation between the overall survival time of CRC patients and the expression of DEGs and TFs. Seven data sets were obtained and 2014 DEGs in CRC were identified. Pathways in cancer and fatty acid metabolism were significantly enriched pathways of upregulated and downregulated DEGs, respectively. Expression of five DEGs (RERGL, ESM1, CA1, ANGPTL7 and TMEFF2) and their five TFs (ZNF354C, ARID3A, NFIC, BRCA1 and ZEB1) was verified by TCGA data sets and qRT-PCR. Their expression in TCGA data sets was same as that in our integrated analysis. Only the expression of EMS1, NFIC, BRCA1 and ZEB1 was inconsistent with integrated analysis and TCGA data sets. Expression of RERGL and BRCA1 was significantly correlated with the overall survival time of CRC patients. These five DEGs may have roles in CRC regulated by their five upstream TFs, which may make a contribution in uncovering the mechanism and providing new strategy of diagnosis and therapies for CRC.
Insights
This study identified 2014 differentially expressed genes (DEGs) in colorectal cancer (CRC) and their regulatory transcription factors (TFs). RERGL and BRCA1 expression correlated with patient survival, offering potential diagnostic and therapeutic strategies for CRC.
Area of Science:
- Genomics
- Cancer Biology
- Bioinformatics
Background:
- Colorectal cancer (CRC) is a significant global health concern.
- Identifying key genes and regulatory factors is crucial for understanding CRC pathogenesis.
- Previous studies have explored gene expression in CRC, but integrated network analysis is needed.
Purpose of the Study:
- To identify differentially expressed genes (DEGs) and their transcription factors (TFs) in colorectal cancer (CRC).
- To construct a CRC-specific transcriptional regulatory network.
- To investigate the correlation between DEG/TF expression and patient survival.
Main Methods:
- Integrated analysis of multiple microarray datasets.
- Functional annotation and pathway enrichment analysis.
- Validation using The Cancer Genome Atlas (TCGA) and qRT-PCR.
- Survival analysis using SurvMicro.
Main Results:
- 2014 DEGs were identified in CRC.
- Upregulated DEGs were enriched in cancer pathways, while downregulated DEGs were linked to fatty acid metabolism.
- Expression of five DEGs (RERGL, ESM1, CA1, ANGPTL7, TMEFF2) and five TFs (ZNF354C, ARID3A, NFIC, BRCA1, ZEB1) was verified.
- Expression of RERGL and BRCA1 significantly correlated with overall survival in CRC patients.
Conclusions:
- Five DEGs and their upstream TFs may play critical roles in CRC development.
- RERGL and BRCA1 hold potential as prognostic biomarkers for CRC.
- Findings may contribute to novel diagnostic and therapeutic strategies for colorectal cancer.
