CMBD: a manually curated cancer metabolic biomarker knowledge database

Area of Science:

• Metabolomics
• Cancer Biology
• Bioinformatics

Background:

• Cancer pathogenesis is driven by complex molecular interactions, including metabolic pathways.
• Metabolic biomarkers offer potential for precise cancer diagnosis, treatment, and prognosis.
• Existing literature on cancer metabolic biomarkers is fragmented, hindering systematic understanding.

Purpose of the Study:

• To develop a comprehensive database (CMBD) integrating scattered cancer metabolic biomarker information.
• To systematically analyze cancer metabolic heterogeneity and identify key metabolic pathways.
• To provide an accessible resource for researchers studying cancer metabolism.

Main Methods:

• Manual curation of metabolic biomarkers and their relationships from PubMed literature.
• Integration of data on 282 biomarkers, 76 cancer subtypes, and 18 tissues.
• Pathway analysis of metabolic biomarkers for breast and prostate cancers as case studies.

Main Results:

• The CMBD database contains 438 curated relationships from 248 publications.
• Key metabolic pathways identified in breast cancer include 'Phenylalanine, tyrosine and tryptophan biosynthesis' and 'primary bile acid biosynthesis'.
• Key metabolic pathways identified in prostate cancer include 'Glyoxylate and dicarboxylate metabolism' and 'citrate cycle (TCA cycle)'.

Conclusions:

• The CMBD database provides a valuable resource for understanding cancer metabolic heterogeneity.
• Identified metabolic pathways offer insights into cancer initiation and progression mechanisms.
• This work facilitates further research into metabolic biomarkers for clinical applications.