Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

9.0K
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...
9.0K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.9K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.9K
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

7.5K
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...
7.5K
Combination Therapies and Personalized Medicine02:50

Combination Therapies and Personalized Medicine

4.9K
Combining two or more treatment methods increases the life span of cancer patients while reducing damage to vital organs or tissue from the overuse of a single treatment. Combination therapy also targets different cancer-inducing pathways, thus reducing the chances of developing resistance to treatment.
The combination of the drug acetazolamide and sulforaphane is a good example of combination therapy to treat cancer. The cells in the interior of a large tumor often die due to the hypoxic and...
4.9K
Loss of Tumor Suppressor Gene Functions01:12

Loss of Tumor Suppressor Gene Functions

4.9K
Tumor suppressor genes are normal genes that can slow down cell division, repair DNA mistakes, or program the cells for apoptosis in case of irreparable damage. Hence, they play an essential role in preventing the proliferation of damaged cells.
When the tumor suppressor genes develop mutations or are lost, cells start growing out of control, leading to cancer. However, a single functional copy of the tumor suppressor gene is enough for the cells to maintain their normal functions and cell...
4.9K
Mouse Models of Cancer Study02:43

Mouse Models of Cancer Study

5.6K
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,...
5.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The BRAINTEASER Datasets: Clinical, Wearable and Environmental Data for ALS & MS Progression Modeling.

Scientific data·2025
Same author

Unleashing the potential of digital pathology data by training computer-aided diagnosis models without human annotations.

NPJ digital medicine·2022
Same author

TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction.

BMC bioinformatics·2022
Same author

MedTAG: a portable and customizable annotation tool for biomedical documents.

BMC medical informatics and decision making·2021
Same author

Search, access, and explore life science nanopublications on the Web.

PeerJ. Computer science·2021
Same journal

Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species.

Database : the journal of biological databases and curation·2026
Same journal

KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.

Database : the journal of biological databases and curation·2026
Same journal

PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.

Database : the journal of biological databases and curation·2026
Same journal

A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs.

Database : the journal of biological databases and curation·2026
Same journal

GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.

Database : the journal of biological databases and curation·2026
Same journal

Rosetta Statements: simplifying FAIR knowledge graph construction with a user-centred approach.

Database : the journal of biological databases and curation·2026
See all related articles

Related Experiment Video

Updated: Jul 15, 2025

Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
08:00

Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal

Published on: October 11, 2019

7.6K

Building a large gene expression-cancer knowledge base with limited human annotations.

Stefano Marchesin1, Laura Menotti1, Fabio Giachelle1

  • 1Department of Information Engineering, University of Padova, Via G. Gradenigo 6b, Padova 35131, Italy.

Database : the Journal of Biological Databases and Curation
|September 28, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces the Collaborative Oriented Relation Extraction (CORE) system to build knowledge bases for cancer research using limited data. CORE enhances data-driven precision medicine by creating a comprehensive gene expression-cancer association knowledge base.

More Related Videos

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
07:41

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

Published on: May 17, 2019

9.0K
Development of Compendium for Esophageal Squamous Cell Carcinoma
03:36

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

479

Related Experiment Videos

Last Updated: Jul 15, 2025

Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
08:00

Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal

Published on: October 11, 2019

7.6K
Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
07:41

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

Published on: May 17, 2019

9.0K
Development of Compendium for Esophageal Squamous Cell Carcinoma
03:36

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

479

Area of Science:

  • Computational biology
  • Bioinformatics
  • Public health

Background:

  • Data-driven research is crucial for advancing cancer prevention and precision medicine.
  • Effective cancer research requires well-organized, machine-readable knowledge bases (KBs).
  • Existing methods for KB construction often demand extensive manual annotation.

Purpose of the Study:

  • To introduce the Collaborative Oriented Relation Extraction (CORE) system for efficient KB construction.
  • To develop the largest KB focused on 'fine-grained' gene expression-cancer associations.
  • To support data-driven precision medicine and validate experimental cancer research.

Main Methods:

  • CORE combines distant supervision and active learning paradigms.
  • The system features a modular, transparent architecture for large-scale processing.
  • Focus on extracting gene expression-cancer associations with limited manual annotations.

Main Results:

  • CORE successfully builds a comprehensive KB of gene expression-cancer associations.
  • The system demonstrates robustness and scalability for large-scale data processing.
  • The generated KB serves as a valuable resource for cancer research.

Conclusions:

  • The CORE system offers an efficient solution for building specialized KBs with minimal manual input.
  • The developed KB significantly contributes to precision medicine by linking gene expression data to cancer.
  • CORE facilitates the validation and complementation of experimental findings in cancer research.