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. 2023 Dec 4;3(1):e155.
doi: 10.1002/imt2.155. eCollection 2024 Feb.

CBD2: A functional biomarker database for colorectal cancer

Xueli Zhang  1   2   3   4 , Min Li  1   5 , Siting Ye  6   7 , Ke Shen  8 , Haining Yuan  9 , Shoaib Bakhtyar  10 , Qiliang Peng  11 , Yongsheng Liu  12 , Yingying Wang  13 , Manshi Li  13 , Chi Zhang  14 , Yixin Wang  5   15 , Xiaohe Bai  16 , Shunming Liu  3 , Ke Zhao  1   2   4   17 , Bairong Shen  18 , Dirk Repsilber  10 , Guang Hu  5 , Hong Zhang  10 , Xiao-Feng Sun  2
Affiliations

CBD2: A functional biomarker database for colorectal cancer

Xueli Zhang et al. Imeta. .

Abstract

The rapidly evolving landscape of biomarkers for colorectal cancer (CRC) necessitates an integrative, updated repository. In response, we constructed the Colorectal Cancer Biomarker Database (CBD), which collected and displayed the curated biomedicine information for 870 CRC biomarkers in the previous study. Building on CBD, we have now developed CBD2, which includes information on 1569 newly reported biomarkers derived from different biological sources (DNA, RNA, protein, and others) and clinical applications (diagnosis, treatment, and prognosis). CBD2 also incorporates information on nonbiomarkers that have been identified as unsuitable for use as biomarkers in CRC. A key new feature of CBD2 is its network analysis function, by which users can investigate the visible and topological network between biomarkers and identify their relevant pathways. CBD2 also allows users to query a series of chemicals, drug combinations, or multiple targets, to enable multidrug, multitarget, multipathway analyses, toward facilitating the design of polypharmacological treatments for CRC. CBD2 is freely available at http://www.eyeseeworld.com/cbd.

Keywords: biomarker; colorectal cancer; database; network analysis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The pipeline of CBD2. We manually collected and classified validated biomarkers and nonbiomarkers by manually reading the literature, and added innovative network construction and analysis functions. CBD, Colorectal Cancer Biomarker Database.
Figure 2
Figure 2
Simple guide on how to use the functions available in CBD2. (A) Three different ways offered by us to retrieve data: Categorical search, Keyword search, and Advanced search. (B) Steps and schematic diagram of the network analysis function module. CBD, Colorectal Cancer Biomarker Database.
Figure 3
Figure 3
Box plot of topological parameters for existing diagnostic, therapeutic, and prognostic protein biomarkers in CBD2. Due to the large differences in the respective groups for Betweenness and Degree, we performed a log transformation on these two parameters. Comparisons labeled as “ns” denote “not significant,” indicating that the statistical tests did not find a significant difference between the compared groups. CBD, Colorectal Cancer Biomarker Database.
Figure 4
Figure 4
ncRNA–gene interaction network of the biomarkers in CBD2. Following the analytical procedure through miRNet, an interactive subset consisting of 713 proteins (genes) and 15 miRNAs was identified from the initial input. (A) The derived network encompasses a total of 6235 genes and 72 miRNAs, forming a complex structure with 13,670 edges. The green nodes represent genes, and the red nodes represent miRNAs. The labels for the miRNAs that rank in the top 10 in terms of degree among all miRNAs are displayed. (B) Basic topological parameter information of the top 10 miRNAs in terms of degree. The miRNA collected in CBD2 is highlighted in orange. CBD, Colorectal Cancer Biomarker Database; miRNA, microRNA; ncRNA, noncoding RNA.
See this image and copyright information in PMC

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