Identification of genes with universally upregulated or downregulated expressions in colorectal cancer
Kai Song
Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
Search for more papers by this authorWei Su
Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
Search for more papers by this authorYanlong Liu
Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
Search for more papers by this authorJiahui Zhang
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorQirui Liang
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorNa Li
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorQingzhou Guan
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorJun He
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorXuefeng Bai
Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
Search for more papers by this authorCorresponding Author
Wenyuan Zhao
Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
Correspondence
Wenyuan Zhao and Zheng Guo, Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
Email: [email protected]; [email protected]
Search for more papers by this authorCorresponding Author
Zheng Guo
Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Correspondence
Wenyuan Zhao and Zheng Guo, Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
Email: [email protected]; [email protected]
Search for more papers by this authorKai Song
Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
Search for more papers by this authorWei Su
Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
Search for more papers by this authorYanlong Liu
Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
Search for more papers by this authorJiahui Zhang
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorQirui Liang
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorNa Li
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorQingzhou Guan
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorJun He
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Search for more papers by this authorXuefeng Bai
Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
Search for more papers by this authorCorresponding Author
Wenyuan Zhao
Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
Correspondence
Wenyuan Zhao and Zheng Guo, Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
Email: [email protected]; [email protected]
Search for more papers by this authorCorresponding Author
Zheng Guo
Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
Correspondence
Wenyuan Zhao and Zheng Guo, Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
Email: [email protected]; [email protected]
Search for more papers by this authorAbstract
Background and Aim
Differentially expressed (DE) genes detected at the population-level through case–control comparison provide no information on the dysregulation frequencies of DE genes in a cancer. In this work, we aimed to identify the genes with universally upregulated or downregulated expressions in colorectal cancer (CRC).
Methods
We firstly clarified that DE genes in an individual cancer tissue should be the disease-relevant genes, which are dysregulated in the cancer tissue in comparison with its own previously normal state. Then, we identified DE genes at the individual level for 2233 CRC samples collected from multiple data sources using the RankComp algorithm.
Results
We found 26 genes that were upregulated or downregulated in almost all the 2233 CRC samples and validated the results using 124 CRC tissues with paired adjacent normal tissues. Especially, we found that two genes (AJUBA and EGFL6), upregulated universally in CRC tissues, were extremely lowly expressed in normal colorectal tissues, which were considered to be oncogenes in CRC oncogenesis and development. Oppositely, we found that one gene (LPAR1), downregulated universally in CRC tissues, was silenced in CRC tissues but highly expressed in normal colorectal tissues, which were considered to be tumor suppressor genes in CRC. Functional evidences revealed that these three genes may induce CRC through deregulating pathways for ribosome biogenesis, cell proliferation, and cell cycle.
Conclusions
In conclusion, the individual-level DE genes analysis can help us find genes dysregulated universally in CRC tissues, which may be important diagnostic biomarkers and therapy targets.
Supporting Information
| Filename | Description |
|---|---|
| JGH14529-sup-0001-sf1.tiffTIFF image, 3.4 MB |
Figure S1. The MAplots for each dataset. |
| JGH14529-sup-0002-sf2.tifTIFF image, 328.9 KB |
Figure S2. The consistency of DE genes identified by T-test and Limma algorithm. (A) DE genes detected in the dataset of GSE23878. (B) DE genes reproducibly detected in the datasets of GSE23878 and GSE31279. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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