Related Experiment Video
Updated: Mar 21, 2026
07:01
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
1.2K
A New Approach for Identification of Cancer-related Pathways using Protein Networks and Genomic Data.
André Fonseca1, Marco D Gubitoso2, Marcelo S Reis3
1Brain Institute, UFRN, Natal, Brazil.
Cancer Informatics
|May 10, 2016
Summary
This study introduces a computational model to analyze static omics data, revealing distinct signaling pathway disturbances in cancer cells. It identifies protein network motifs specific to breast cancer subtypes, aiding in understanding cancer cell control systems.
Area of Science:
- Computational biology
- Cancer research
- Systems biology
Background:
- Cancer cells exhibit abnormal growth due to disrupted cellular control systems.
- High-throughput dynamical data for studying these systems is scarce.
- Static omics data and biological knowledge offer an alternative approach.
Purpose of the Study:
- To develop a method for extracting insights into cancer cell control systems using static omics data.
- To investigate differences in signaling pathways across cancer cell types.
- To identify novel cancer-related genes and pathways.
Main Methods:
- Integration of gene expression profiles and signaling pathway data.
- Development and application of a statistical computational model.
- Method for recovering differentially represented protein network motifs.
Main Results:
- The model successfully extracts information from static omics data.
- Identified distinct signaling pathway disturbances in different cancer cell types.
- Discovered protein network motifs specific to breast cancer subtypes, enriched with gene ontologies and potential cancer genes.
Conclusions:
- Static omics data can be leveraged to understand cellular control system disturbances in cancer.
- The developed computational framework and motif recovery method are effective tools for cancer research.
- Findings highlight specific molecular mechanisms and potential therapeutic targets in breast cancer subtypes.
Related Concept Videos
02:26Protein Networks
4.7K
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,...
4.7K
02:26Protein Networks
2.9K
2.9K
03:03mTOR Signaling and Cancer Progression
5.0K
The mammalian target of rapamycin or mTOR protein was discovered in 1994 due to its direct interaction with rapamycin. The protein gets its name from a yeast homolog called TOR. The mTOR protein complex in mammalian cells plays a major role in balancing anabolic processes such as the synthesis of proteins, lipids, and nucleotides and catabolic processes, such as autophagy in response to environmental cues, such as availability of nutrients and growth factors.
The mTOR pathway or the...
The mTOR pathway or the...
5.0K
03:03mTOR Signaling and Cancer Progression
1.6K
1.6K
01:33Cancer-Critical Genes I: Proto-oncogenes
11.8K
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...
11.8K
01:21Cancer Survival Analysis
819
Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
819