MACC: a visual interactive knowledgebase of metabolite-associated cell communications.

Journal: Nucleic acids research
PMID: 37897362

Abstract

Metabolite-associated cell communications play critical roles in maintaining the normal biological function of human through coordinating cells, organs and physiological systems. Though substantial information of MACCs has been continuously reported, no relevant database has become available so far. To address this gap, we here developed the first knowledgebase (MACC), to comprehensively describe human metabolite-associated cell communications through curation of experimental literatures. MACC currently contains: (a) 4206 carefully curated metabolite-associated cell communications pairs involving 244 human endogenous metabolites and reported biological effects in vivo and in vitro; (b) 226 comprehensive cell subtypes and 296 disease states, such as cancers, autoimmune diseases, and pathogenic infections; (c) 4508 metabolite-related enzymes and transporters, involving 542 pathways; (d) an interactive tool with user-friendly interface to visualize networks of multiple metabolite-cell interactions. (e) overall expression landscape of metabolite-associated gene sets derived from over 1500 single-cell expression profiles to infer metabolites variations across different cells in the sample. Also, MACC enables cross-links to well-known databases, such as HMDB, DrugBank, TTD and PubMed etc. In complement to ligand-receptor databases, MACC may give new perspectives of alternative communication between cells via metabolite secretion and adsorption, together with the resulting biological functions. MACC is publicly accessible at: http://macc.badd-cao.net/.

Authors

  • Jian Gao
  • Saifeng Mo
    Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
  • Jun Wang
    Department of Speech, Language, and Hearing Sciences and the Department of Neurology, The University of Texas at Austin, Austin, TX 78712, USA.
  • Mou Zhang
    School of Life Sciences, Fudan University, Shanghai, China.
  • Yao Shi
    Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; Yunnan Technical Center for Quality of Chinese Materia Medica, Kunming 650200, China.
  • Chuhan Zhu
    Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
  • Yuxuan Shang
    Biological Sciences, University of California Santa Barbara, CA, USA.
  • Xinyue Tang
    Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
  • Shiyue Zhang
    School of Life Sciences, Fudan University, Shanghai, China.
  • Xinwen Wu
    Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
  • Xinyan Xu
    Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
  • Yiheng Wang
    School of Computing, University of Southern Mississippi, 118 College Drive #5106, Hattiesburg, Mississippi 39406-0001.
  • Zihao Li
    School of Mechanical Engineering and Automation, Harbin Institute of Technology(Shenzhen), Shenzhen, 518055, China.
  • Genhui Zheng
    Dept. of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
  • Zikun Chen
    Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
  • Qiming Wang
    School of Life Sciences, Fudan University, Shanghai, China.
  • Kailin Tang
    Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
  • Zhiwei Cao
    Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

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