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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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.
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.
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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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Updated: Jun 28, 2026

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

Annotating breast cancer microarray samples using ontologies.

Hongfang Liu1, Xin Li, Victoria Yoon

  • 1Lombardi Comprehensive Cancer Center, Georgetown University Medical Center,Washington, DC, USA.

AMIA ... Annual Symposium Proceedings. AMIA Symposium
|November 13, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces BCM-CO, an ontology for breast cancer microarray data. It improves upon existing standards by incorporating more comprehensive clinical and research terms for better data indexing and retrieval.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Breast cancer is the most common cancer in women, driven by gene mutations.
  • High-throughput gene expression microarrays aid in diagnosis, prognosis, and treatment prediction.
  • Existing microarray data annotation faces inconsistencies due to high dimensionality and data accessibility.

Purpose of the Study:

  • To develop BCM-CO, an ontology for indexing clinical annotations of breast cancer microarray samples.
  • To address the limited coverage of NCI Thesaurus for breast cancer-specific terms.
  • To enhance the retrieval of breast cancer microarray data.

Main Methods:

  • Developed BCM-CO ontology tailored for breast cancer microarray clinical annotations.
  • Incorporated broader terms for histology, cell lines, grading, and staging.
  • Indexed samples from Gene Expression Omnibus (GEO) using BCM-CO and MGED ontology.
  • Created a web-based prototype system for data retrieval.

Main Results:

  • NCI Thesaurus coverage was limited for key breast cancer descriptors (histology, cell lines, grading, staging).
  • BCM-CO successfully indexed breast cancer microarray samples from GEO.
  • A functional prototype system was developed for ontology-based data retrieval.

Conclusions:

  • BCM-CO enhances the annotation and retrieval of breast cancer microarray data.
  • The developed ontology addresses limitations in existing terminologies for breast cancer research.
  • The prototype system facilitates more effective access to valuable breast cancer genomic data.