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CCCdb: a comprehensive manually curated database for cell-cell communication in human and mouse.

Mingcong Xu1,2, Guorui Zhang1, Xuan Wang1

  • 1The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.

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This study introduces CCCdb, a manually curated database of experimentally validated cell-cell communication (CCC) in humans and mice. CCCdb provides a comprehensive resource for understanding tissue homeostasis and disease mechanisms.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Cell-cell communication (CCC) is crucial for multicellular organism organization, function, and plasticity.
  • Advancing experimental technologies necessitate curated, experimentally validated CCC data across diverse biological contexts.
  • Understanding complex multicellular systems and disease microenvironments requires systematic data on CCC.

Purpose of the Study:

  • To present CCCdb, a comprehensive, manually curated database of experimentally validated CCCs for human and mouse.
  • To provide standardized annotations for cell types, tissues, and phenotypes involved in CCC.
  • To enhance accessibility and biological interpretability of CCC data through an AI assistant.

Main Methods:

  • Manual curation of thousands of publications to extract CCC information.
  • Systematic annotation of 8467 CCC entries with standardized data on cell types, tissues, and phenotypes.
  • Integration of a ReAct-based AI assistant for natural-language querying and navigation.

Main Results:

  • CCCdb contains 8467 experimentally validated CCC entries for human and mouse.
  • The database covers 98 tissues, 1132 cell types, and 548 phenotypes.
  • CCCs are mediated through direct contact, autocrine, paracrine, and endocrine signaling.

Conclusions:

  • CCCdb serves as a foundational resource for studying CCC.
  • The database facilitates elucidation of mechanisms underlying tissue homeostasis and disease progression.
  • The integrated AI assistant enhances user interaction and data interpretation.