Related Experiment Video

Updated: Oct 20, 2025

Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
08:08

Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors

Published on: February 27, 2015

16.5K

Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis

Daejin Hyung1, Min-Jeong Baek1, Jongkeun Lee1

  • 1National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea.

Computational and Structural Biotechnology Journal
|September 10, 2021
PubMed

Insights

Researchers developed the Protein-gene Expression Nexus (PEN), a proteogenomic database integrating multi-omics data from 145 cancer cell lines. This resource accelerates cancer research by providing insights into molecular features driving oncogenic modulation.

Area of Science:

  • Cancer Research
  • Proteogenomics
  • Multi-omics

Background:

  • Understanding molecular features of oncogenic modulation in cancer is crucial for therapeutic insights.
  • Multi-omics approaches studying DNA, RNA, and proteins in human cancer cell lines offer new therapeutic avenues.

Purpose of the Study:

  • To develop a comprehensive proteogenomic database for human cancer cell lines to enhance understanding of molecular features associated with oncogenic modulation.
  • To integrate genetic, mRNA, and protein data from diverse cancer cell line studies.

Main Methods:

  • Expanded characterization of 145 cancer cell lines with genetic, mRNA, and protein data from public studies.
  • Compiled proteomic and phosphoproteomic data, including peptides, proteins, and phosphorylation site-associated genomic variations.
  • Analyzed functional characterizations and integrated datasets, including copy number alteration (CNA), single amino acid variation, and post-translation modification site variation.

Main Results:

  • The Protein-gene Expression Nexus (PEN) database integrates data from 117 studies across 12 cancer types.
  • PEN contains extensive proteomic and phosphoproteomic data, encompassing millions of peptides and thousands of proteins and genomic variations.
  • Functional analyses revealed associations between CNA, gene expression, and novel peptide expression.

Conclusions:

  • The PEN database and data portal serve as a valuable resource for accelerating cancer research.
  • Provides a user-friendly platform for data exploration, visualization, and download to facilitate discovery.
  • Facilitates research on model cancer cell lines for improved therapeutic strategies.
Keywords:
Cancer cell linePhosphoproteomicsProteogenomicsSingle amino acid variationSystems biology

More Related Videos

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

12.2K
Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases07:41

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

Published on: May 17, 2019

9.2K

Related Concept Videos

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...
9.3K
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...
8.4K
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,...
4.2K
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
8.5K