Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb.
BMC Biol
; 22(1): 152, 2024 Jul 08.
Article
in En
| MEDLINE
| ID: mdl-38978014
ABSTRACT
BACKGROUND:
Metabolite-associated cell communications play critical roles in maintaining human biological function. However, most existing tools and resources focus only on ligand-receptor interaction pairs where both partners are proteinaceous, neglecting other non-protein molecules. To address this gap, we introduce the MRCLinkdb database and algorithm, which aggregates and organizes data related to non-protein L-R interactions in cell-cell communication, providing a valuable resource for predicting intercellular communication based on metabolite-related ligand-receptor interactions.RESULTS:
Here, we manually curated the metabolite-ligand-receptor (ML-R) interactions from the literature and known databases, ultimately collecting over 790 human and 670 mouse ML-R interactions. Additionally, we compiled information on over 1900 enzymes and 260 transporter entries associated with these metabolites. We developed Metabolite-Receptor based Cell Link Database (MRCLinkdb) to store these ML-R interactions data. Meanwhile, the platform also offers extensive information for presenting ML-R interactions, including fundamental metabolite information and the overall expression landscape of metabolite-associated gene sets (such as receptor, enzymes, and transporter proteins) based on single-cell transcriptomics sequencing (covering 35 human and 26 mouse tissues, 52 human and 44 mouse cell types) and bulk RNA-seq/microarray data (encompassing 62 human and 39 mouse tissues). Furthermore, MRCLinkdb introduces a web server dedicated to the analysis of intercellular communication based on ML-R interactions. MRCLinkdb is freely available at https//www.cellknowledge.com.cn/mrclinkdb/ .CONCLUSIONS:
In addition to supplementing ligand-receptor databases, MRCLinkdb may provide new perspectives for decoding the intercellular communication and advancing related prediction tools based on ML-R interactions.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Cell Communication
Limits:
Animals
/
Humans
Language:
En
Journal:
BMC Biol
Journal subject:
BIOLOGIA
Year:
2024
Document type:
Article
Affiliation country:
Country of publication: