Related Experiment Video
Updated: Aug 1, 2026
13:19
Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
Published on: November 2, 2013
16.6K
CBioProfiler: A Web and Standalone Pipeline for Cancer Biomarker and Subtype Characterization
Xiaoping Liu1,2,3, Zisong Wang1, Hongjie Shi3,4
1Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
Genomics, Proteomics & Bioinformatics
|June 13, 2024
Summary
A new tool, Cancer Biomarker and subtype Profiler (CBioProfiler), aids in identifying cancer biomarkers and subtypes to predict patient survival. This resource offers standardized pipelines and curated data for improved cancer research and clinical applications.
Area of Science:
- Oncology
- Bioinformatics
- Computational Biology
Background:
- Cancer remains a major global health challenge, necessitating accurate prediction of patient survival for effective treatment and prognosis.
- Current tools for exploring cancer biomarkers and subtypes lack standardization, hindering research and clinical application.
Purpose of the Study:
- To introduce Cancer Biomarker and subtype Profiler (CBioProfiler), a novel web server and standalone application.
- To provide standardized pipelines for analyzing cancer biomarkers and subtypes to predict patient survival.
Main Methods:
- Developed two distinct pipelines: one for cancer biomarker identification and annotation using machine learning, and another for cancer subtype identification using unsupervised learning.
- Integrated CuratedCancerPrognosisData, an R package with curated gene expression and clinical data from 268 studies covering 43 tumor types and 47,686 samples.
Main Results:
- CBioProfiler offers a comprehensive platform for analyzing cancer survival-related biomarkers and identifying distinct cancer subtypes.
- The integrated dataset provides a robust resource for validating findings across a wide range of cancer types.
Conclusions:
- CBioProfiler addresses the need for standardized tools in cancer biomarker and subtype analysis.
- This resource facilitates improved risk stratification, treatment selection, and prognostic assessment for cancer patients.
More Related Videos
Related Concept Videos
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:07Tumor Progression
Tumor progression is a phenomenon where the pre-formed tumor acquires successive mutations to become clinically more aggressive and malignant. In the 1950s, Foulds first described the stepwise progression of cancer cells through successive stages.
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
Colon cancer is one of the best-documented examples of tumor progression. Early mutation in the APC gene in colon cells causes a small growth on the colon wall called a polyp. With time, this polyp grows into a benign, pre-cancerous tumor. Further...
01:33Cancer-Critical Genes I: Proto-oncogenes
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...