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Related Concept Videos

Protein Networks02:26

Protein 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,...
Protein Networks02:26

Protein 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,...
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...
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...
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...
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...

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Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres
06:52

Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres

Published on: July 22, 2020

Predicting genes involved in human cancer using network contextual information.

Hossein Rahmani1, Hendrik Blockeel, Andreas Bender

  • 1Leiden Institute of Advanced Computer Science, Universiteit Leiden, Niels Bohrweg 1, 2333 CA Leiden, The Netherlands. hrahmani@liacs.nl

Journal of Integrative Bioinformatics
|September 6, 2012
PubMed
Summary

This study introduces novel functional and structural context features for predicting cancer-associated proteins using protein-protein interaction (PPI) networks. These new features significantly improve prediction accuracy over existing methods.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Network Science

Background:

  • Protein-Protein Interaction (PPI) networks are crucial for identifying proteins implicated in cancer.
  • Existing prediction methods utilize protein function, network proximity, and local network structure.

Purpose of the Study:

  • To introduce novel functional and structural context features for enhanced protein function prediction in cancer.
  • To develop a feature selection strategy for identifying the most informative features.

Main Methods:

  • Incorporated 'Functional Context' (functions of interacting proteins) and 'Structural Context' (relative positions based on ANOVA) as new input features.
  • Implemented a feature selection strategy to pinpoint informative features.
  • Utilized a Naive Bayes machine learning model for prediction.

Main Results:

  • The proposed features and selection strategy yielded highly informative inputs.
  • The Naive Bayes model with new features outperformed state-of-the-art methods by over 5% in F-measure.
  • Manual inspection validated the biological relevance of the top-ranked features.

Conclusions:

  • Novel functional and structural context features significantly enhance cancer-related protein prediction.
  • The developed feature selection strategy is effective in identifying key predictive features.
  • This approach offers a more accurate and biologically relevant method for cancer protein prediction using PPI networks.