ArticleDatabase : the journal of biological databases and curation2023
CCIDB: a manually curated cell-cell interaction database with cell context information.
Article in Database : the journal of biological databases and curation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Navigating cell maps by deep learning integration of single-cell and spatially resolved transcriptomics.Briefings in bioinformatics · 2026Article
- Reconstructing cell-cell interaction network in single-cell spatial transcriptomics via directed heterogeneous graph autoencoder.Bioinformatics (Oxford, England) · 2026Article
- CCCdb: a comprehensive manually curated database for cell-cell communication in human and mouse.Nucleic acids research · 2026Article
- Multidimensional tumor-blood profiling uncovers systemic lymphocyte-monocyte imbalance in pituitary neuroendocrine tumors.Signal transduction and targeted therapy · 2025Article
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- Causal machine learning for single-cell genomics.Nature genetics · 2025Review
- Elucidating the mechanistic relationships between peroxisome proliferator-activated receptors and hepatic fibrosis using the ROBOKOP knowledge graph.Frontiers in toxicology · 2025Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-cell interaction (CCI) is a crucial event in the development and function of multicellular organisms. The development of CCI databases is beneficial for researchers who want to analyze single-cell sequencing data or study CCI through molecular experiments. CCIs are known to act differently according to cellular and biological contexts such as cell types, gene mutations or disease status; however, previous CCI databases do not completely provide this contextual information pertaining to CCIs. We constructed a cell-cell interaction database (CCIDB) containing the biological and clinical contexts involved in each interaction. To build a database of cellular and tissue contexts, we collected 38 types of context features, which were categorized into seven categories, including 'interaction', 'cell type', 'cofactor', 'effector', 'phenotype', 'pathology' and 'reference'. CCIs were manually retrieved from 272 studies published recently (less than 6 years ago). In the current version of CCIDB, 520 CCIs and their 38 context features have been manually collected and curated by biodata engineers. We suggest that CCIDB is a manually curated CCI resource that is highly useful, especially for analyzing context-dependent alterations in CCIs. Database URL https://ccidb.sysmed.kr/.
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