Related Experiment Video

Updated: Dec 31, 2025

Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts
10:27

Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts

Published on: July 25, 2020

7.7K

ZDOG: zooming in on dominating genes with mutations in cancer pathways

Rudi Alberts1, Jinyu Chen2, Louxin Zhang3

  • 1Department of Mathematics and Computational Biology Programme, National University of Singapore, Singapore, 119076, Singapore. rudi.alberts@nus.edu.sg.

BMC Bioinformatics
|January 1, 2020
PubMed
Abstract

Insights

Identifying cancer-causing genes is difficult due to mutation heterogeneity. ZDOG, a Cytoscape app, visualizes mutated gene impact on cancer pathways using a dominating tree model, aiding master regulator discovery.

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Cancer Genomics

Background:

  • Somatic mutation heterogeneity poses challenges in identifying cancer-causing genes and their functions.
  • Many cancer-driving genes exhibit rare mutations, complicating traditional analysis.

Purpose of the Study:

  • To develop a computational tool for visualizing the impact of mutated genes on cancer pathways.
  • To facilitate the identification of key regulatory genes, even those with low mutation frequencies.

Main Methods:

  • Development of the ZDOG Cytoscape application.
  • Utilizing a dominating tree model to analyze gene positional importance within signalling pathways.

Main Results:

  • The ZDOG app enables visualization of how mutated genes affect cancer pathways.
  • The dominating tree model effectively identifies critical mutated "master" regulators in deregulated pathways.
  • The tool aids in understanding the downstream effects of gene mutations.

Conclusions:

  • A novel model and user-friendly Cytoscape app (ZDOG) have been developed to assess mutation impact on signalling pathways.
  • ZDOG facilitates the examination of a gene's positional influence on downstream pathway components.
  • The ZDOG app is freely available for use and installation via GitHub and the Cytoscape App Store.
Keywords:
Cancer-causing genesCytoscape appDominator treePI3K/AKT signalling

More Related Videos

Integration of Bioinformatics Approaches and Experimental Validations to Understand the Role of Notch Signaling in Ovarian Cancer09:08

Integration of Bioinformatics Approaches and Experimental Validations to Understand the Role of Notch Signaling in Ovarian Cancer

Published on: January 12, 2020

7.1K
A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis07:41

A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis

Published on: March 8, 2022

2.8K

Related Concept Videos

Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-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...
11.0K
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

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...
9.3K
Cancers Originate from Somatic Mutations in a Single Cell02:21

Cancers Originate from Somatic Mutations in a Single Cell

Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
14.4K
Adaptive Mechanisms in Cancer Cells02:53

Adaptive Mechanisms in Cancer Cells

Cancer cells accumulate genetic changes at an abnormally rapid rate due to the defects in the DNA repair mechanisms. From an evolutionary perspective, such genetic instability is advantageous for cancer development. Mutant cell lines accumulate a series of beneficial mutations that contribute to their progression into cancer.
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...
6.8K
Mouse Models of Cancer Study02:43

Mouse Models of Cancer Study

Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
6.3K