NDLI: Discovering the molecular differences between right- and left-sided colon cancer using machine learning methods

Content Provider	Springer Nature : BioMed Central
Author	Jiang, Yimei Yan, Xiaowei Liu, Kun Shi, Yiqing Wang, Changgang Hu, Jiele Li, You Wu, Qinghua Xiang, Ming Zhao, Ren
Abstract	Background In recent years, the differences between left-sided colon cancer (LCC) and right-sided colon cancer (RCC) have received increasing attention due to the clinicopathological variation between them. However, some of these differences have remained unclear and conflicting results have been reported. Methods From The Cancer Genome Atlas (TCGA), we obtained RNA sequencing data and gene mutation data on 323 and 283 colon cancer patients, respectively. Differential analysis was firstly done on gene expression data and mutation data between LCC and RCC, separately. Machine learning (ML) methods were then used to select key genes or mutations as features to construct models to classify LCC and RCC patients. Finally, we conducted correlation analysis to identify the correlations between differentially expressed genes (DEGs) and mutations using logistic regression (LR) models. Results We found distinct gene mutation and expression patterns between LCC and RCC patients and further selected the 30 most important mutations and 17 most important gene expression features using ML methods. The classification models created using these features classified LCC and RCC patients with high accuracy (areas under the curve (AUC) of 0.8 and 0.96 for mutation and gene expression data, respectively). The expression of PRAC1 and BRAF V600E mutation (rs113488022) were the most important feature for each model. Correlations of mutations and gene expression data were also identified using LR models. Among them, rs113488022 was found to have significance relevance to the expression of four genes, and thus should be focused on in further study. Conclusions On the basis of ML methods, we found some key molecular differences between LCC and RCC, which could differentiate these two groups of patients with high accuracy. These differences might be key factors behind the variation in clinical features between LCC and RCC and thus help to improve treatment, such as determining the appropriate therapy for patients.
Related Links	https://bmccancer.biomedcentral.com/counter/pdf/10.1186/s12885-020-07507-8.pdf
Ending Page	11
Page Count	11
Starting Page	1
File Format	HTM / HTML
ISSN	14712407
DOI	10.1186/s12885-020-07507-8
Journal	BMC Cancer
Issue Number	1
Volume Number	20
Language	English
Publisher	BioMed Central
Publisher Date	2020-10-19
Access Restriction	Open
Subject Keyword	Cancer Research Oncology Surgical Oncology Health Promotion and Disease Prevention Biomedicine Medicine Public Health Left-sided colon cancer Right-sided colon cancer Machine learning Mutations Gene expression Medicine/Public Health
Content Type	Text
Resource Type	Article
Subject	Cancer Research Oncology Genetics
Journal Impact Factor	3.4/2023
5-Year Journal Impact Factor	3.8/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Better survival in right-sided versus left-sided stage I - III colon cancer patients

Identifying important microbial and genomic biomarkers for differentiating right- versus left-sided colorectal cancer using random forest models

Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression

Prognostic value of total number of lymph nodes retrieved differs between left-sided colon cancer and right-sided colon cancer in stage III patients with colon cancer

Clinical baseline and prognostic difference of platelet lymphocyte ratio (PLR) in right-sided and let-sided colon cancers

PTEN mRNA expression is less pronounced in left- than right-sided colon cancer: a retrospective observational study

SOX2 expression correlates with lymph-node metastases and distant spread in right-sided colon cancer

Second primary colorectal cancer after the initial primary colorectal cancer

Large differences in global transcriptional regulatory programs of normal and tumor colon cells

Discovering the molecular differences between right- and left-sided colon cancer using machine learning methods

Similar Documents

Better survival in right-sided versus left-sided stage I - III colon cancer patients

Identifying important microbial and genomic biomarkers for differentiating right- versus left-sided colorectal cancer using random forest models

Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression

Prognostic value of total number of lymph nodes retrieved differs between left-sided colon cancer and right-sided colon cancer in stage III patients with colon cancer

Clinical baseline and prognostic difference of platelet lymphocyte ratio (PLR) in right-sided and let-sided colon cancers

PTEN mRNA expression is less pronounced in left- than right-sided colon cancer: a retrospective observational study

SOX2 expression correlates with lymph-node metastases and distant spread in right-sided colon cancer

Second primary colorectal cancer after the initial primary colorectal cancer

Large differences in global transcriptional regulatory programs of normal and tumor colon cells

Discovering the molecular differences between right- and left-sided colon cancer using machine learning methods