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CCIDB: a manually curated cell-cell interaction database with cell context information.

Jin Young Noh1,2,3, Hae In Lee1,2,3, Ji-Hye Choi1,2

  • 1Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.

Database : the Journal of Biological Databases and Curation
|August 11, 2023
PubMed
Summary

Researchers have developed a new Cell-Cell Interaction Database (CCIDB) to analyze how cellular and biological contexts affect cell-cell interactions (CCIs). This manually curated resource provides crucial contextual information for studying CCIs in various biological and clinical settings.

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Area of Science:

  • Systems biology
  • Bioinformatics
  • Genomics

Background:

  • Cell-cell interaction (CCI) is fundamental for multicellular organisms.
  • Existing CCI databases lack comprehensive contextual information.
  • Context (cell type, disease) significantly influences CCI.

Purpose of the Study:

  • To create a manually curated Cell-Cell Interaction Database (CCIDB).
  • To incorporate biological and clinical context into CCI data.
  • To facilitate the analysis of context-dependent CCIs.

Main Methods:

  • Collected 38 context features across seven categories.
  • Manually curated 520 CCIs from 272 recent studies.
  • Integrated interaction, cell type, cofactor, effector, phenotype, pathology, and reference data.

Main Results:

  • CCIDB version 1 contains 520 manually curated CCIs.
  • Each CCI is annotated with 38 distinct context features.
  • The database provides detailed biological and clinical context for CCIs.

Conclusions:

  • CCIDB offers a valuable resource for researchers studying CCIs.
  • The database enables analysis of context-specific CCI alterations.
  • CCIDB supports advanced research in single-cell sequencing and molecular biology.