Network-based identification of biomarkers for colon adenocarcinoma
Background: As one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges.
Methods: We firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively.
Results: Classification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD.
Conclusions: In conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD. And the subtypes could be used in realizing the personalized medicine of COAD.
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Posted 12 May, 2020
On 17 Jul, 2020
On 27 Apr, 2020
On 26 Apr, 2020
On 14 Feb, 2020
On 31 Mar, 2020
Received 23 Mar, 2020
Received 15 Mar, 2020
On 03 Mar, 2020
On 02 Mar, 2020
On 02 Mar, 2020
On 02 Mar, 2020
Invitations sent on 29 Feb, 2020
On 11 Feb, 2020
On 10 Feb, 2020
On 10 Feb, 2020
On 08 Feb, 2020
Network-based identification of biomarkers for colon adenocarcinoma
Posted 12 May, 2020
On 17 Jul, 2020
On 27 Apr, 2020
On 26 Apr, 2020
On 14 Feb, 2020
On 31 Mar, 2020
Received 23 Mar, 2020
Received 15 Mar, 2020
On 03 Mar, 2020
On 02 Mar, 2020
On 02 Mar, 2020
On 02 Mar, 2020
Invitations sent on 29 Feb, 2020
On 11 Feb, 2020
On 10 Feb, 2020
On 10 Feb, 2020
On 08 Feb, 2020
Background: As one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges.
Methods: We firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively.
Results: Classification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD.
Conclusions: In conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD. And the subtypes could be used in realizing the personalized medicine of COAD.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7