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Related Concept Videos

What is Cell Signaling?02:03

What is Cell Signaling?

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Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate to respond to the environment.
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Overview of Cell Signaling01:23

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Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
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Interactions Between Signaling Pathways01:19

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Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
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The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity. 
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Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. The continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors, which cannot interact with most components of the cell, such as DNA. Only internal receptors can interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the...
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The extracellular matrix or ECM holds cells together to form a tissue and allows the cells within the tissue to communicate. ECM comprises proteins such as fibronectin, collagen, laminin, etc. The most abundant protein in this space is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. ECM allows cell migration and provides a structural scaffold at cell adhesion that anchors the cell when the extracellular matrix proteins interact with...
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Updated: Nov 12, 2025

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

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Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.

Dénes Türei1, Alberto Valdeolivas1, Lejla Gul2

  • 1Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany.

Molecular Systems Biology
|March 22, 2021
PubMed
Summary
This summary is machine-generated.

OmniPath integrates over 100 resources to map intercellular communication and intracellular signaling pathways. This comprehensive knowledge base aids in understanding cell-cell interactions and their downstream effects in biological data analysis.

Keywords:
intercellular signalingligand-receptor interactionsomics integrationpathwayssignaling network

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Area of Science:

  • Systems Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • Molecular knowledge is crucial for omics data analysis, particularly for understanding cellular mechanisms and interactions.
  • Existing resources for intercellular communication are fragmented and lack integration with intracellular processes.
  • A unified resource is needed to link cell-cell communication with intracellular signaling pathways.

Purpose of the Study:

  • To create a comprehensive, integrated resource for molecular knowledge of inter- and intracellular signaling.
  • To facilitate the analysis of cell-cell interactions and their downstream effects on intracellular processes.
  • To provide accessible tools and data for computational and experimental scientists.

Main Methods:

  • Integrated over 100 databases covering protein interactions, roles in signaling, transcriptional/post-transcriptional regulation.
  • Added protein complex information, functional annotations, localization, and disease associations.
  • Developed web services, Cytoscape plug-ins, and R/Bioconductor and Python packages for data access.

Main Results:

  • Developed OmniPath, a unified resource linking intercellular communication with intracellular signaling.
  • The resource covers human, mouse, and rat proteomes.
  • Provided workflows and tutorials for analyzing cell-cell interactions and downstream signaling.

Conclusions:

  • OmniPath offers a single access point to integrated molecular knowledge for omics data analysis.
  • The resource enables mechanistic insights into cellular processes, exemplified by studies on SARS-CoV-2 infection and ulcerative colitis.
  • Facilitates advanced analyses of cell communication and intracellular responses.