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Protein Networks

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,...

Proteomics

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...

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Updated: Aug 6, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Gene function and cell surface protein association analysis based on single-cell multiomics data.

Huan Hu¹, Zhen Feng², Hai Lin³

¹Department of Physics, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, 361005, China; National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, 361005, China; Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, 325001, China.

Computers in Biology and Medicine

|March 16, 2023

Summary

This summary is machine-generated.

This study introduces Gene Function and Protein Association (GFPA), a new framework for analyzing single-cell multimodal data. GFPA reveals reliable gene-protein associations, enhancing our understanding of cellular heterogeneity at the protein level.

Keywords:

Association analysis Cell surface protein Computing framework Multiomics Single-cell

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Glycopeptide Capture for Cell Surface Proteomics

Glycopeptide Capture for Cell Surface Proteomics

Published on: May 9, 2014

Area of Science:

Single-cell biology
Proteomics
Bioinformatics

Background:

Single-cell transcriptomics reveals cellular heterogeneity but lacks protein-level insights.
Existing single-cell multiomics studies often prioritize data integration over deep multiomics exploitation.
Understanding cell surface protein associations is crucial for deciphering cellular functions.

Purpose of the Study:

To introduce a novel analysis framework, Gene Function and Protein Association (GFPA), for single-cell multimodal data.
To establish reliable associations between gene function and cell surface proteins.
To overcome limitations of transcriptomics-only approaches in revealing protein-level cellular heterogeneity.

Main Methods:

Development of the Gene Function and Protein Association (GFPA) computational framework.
Application of GFPA to analyze single-cell multimodal data from human peripheral blood mononuclear cells (PBMCs).
Validation of GFPA's reliability across diverse cell subtypes and PBMC samples.

Main Results:

GFPA successfully mines reliable associations between gene function and cell surface proteins.
An association between epithelial mesenchymal transition (EMT) and CD99 protein in CD4 T cells was identified, consistent with prior research.
The GFPA framework demonstrated robustness and reliability across multiple cell subtypes and PBMC samples.

Conclusions:

GFPA provides a powerful new approach for uncovering gene-protein relationships in single-cell multimodal datasets.
The framework enhances the understanding of cellular heterogeneity by integrating gene function and protein expression data.
GFPA offers a reliable tool for researchers studying cell surface proteins and their functional implications.