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Related Concept Videos

Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

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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.
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Related Experiment Video

Updated: Jul 18, 2025

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
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A proteogenomics data-driven knowledge base of human cancer.

Yuxing Liao1, Sara R Savage1, Yongchao Dou1

  • 1Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

Cell Systems
|August 24, 2023
PubMed
Summary
This summary is machine-generated.

LinkedOmicsKB offers a public knowledge base for cancer proteogenomics data, integrating genomics and proteomics. This resource accelerates discoveries for improved cancer understanding and treatment.

Keywords:
CPTACcancerdata integrationknowledge basemulti-omicspan-cancerphosphoproteomicsproteogenomicsproteomicsvisualization

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Area of Science:

  • Oncology
  • Bioinformatics
  • Genomics

Background:

  • Proteogenomics integrates multi-omics data for comprehensive cancer molecular profiling.
  • The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has generated extensive pan-cancer proteogenomics data.

Purpose of the Study:

  • To present LinkedOmicsKB, a novel knowledge base for publicly accessible CPTAC proteogenomics data.
  • To facilitate exploration and discovery in cancer research through an integrated data platform.

Main Methods:

  • Development of a proteogenomics data-driven knowledge base (LinkedOmicsKB).
  • Systematic precomputation and consistent processing of CPTAC pan-cancer proteogenomics data.
  • Creation of gene-, protein-, mutation-, and phenotype-centric web pages with visualization tools.

Main Results:

  • LinkedOmicsKB provides access to precomputed data for 19,701 coding genes, 125,969 phosphosites, and 256 genotypes/phenotypes.
  • Case studies demonstrate LinkedOmicsKB's utility in uncovering novel insights into cancer biology.
  • The platform enables efficient exploration of complex, interconnected proteogenomics data.

Conclusions:

  • LinkedOmicsKB serves as a comprehensive resource for accelerating proteogenomics discoveries.
  • The knowledge base aims to improve the understanding and treatment of human cancer.
  • Publicly available, systematically processed data enhances collaborative research in cancer.