ProCanBio: a database of manually curated biomarkers for Prostate Cancer
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# ProCanBio: A Database of Manually Curated Biomarkers for Prostate Cancer ## Overview ProCanBio is a manually curated database developed for maintaining comprehensive information about biomarkers associated with Prostate Cancer. The database integrates biomarker information collected from published literature and provides detailed annotations regarding: - Diagnostic biomarkers- Prognostic biomarkers- Predictive biomarkers- Genomics data- Proteomics data- Metabolomics data- Epigenomics data ProCanBio was developed to provide a centralized resource for prostate cancer biomarker research and analysis. --- # Research Paper Details ## Title ProCanBio: a database of manually curated biomarkers for Prostate Cancer ## Authors - Dikscha Sapra- Harpreet Kaur- Anjali Dhall- Gajendra P. S. Raghava ## Published Date 10 december 2021 ## DOIhttps://doi.org/10.1089/cmb.2021.0348 https://github.com/Piyushh1104/ProCanBio.git --- # Background Prostate Cancer is one of the most common malignancies in men worldwide and is associated with high mortality. Traditional biomarkers such as: - PSA (Prostate Specific Antigen) lack sufficient specificity because elevated PSA levels are also associated with: - Benign Prostatic Hyperplasia (BPH)- Prostatitis- Prostatic Intraepithelial Neoplasia (PIN) Therefore, there is a need for more reliable biomarkers for: - Diagnosis- Prognosis- Therapeutic response prediction Although numerous studies have identified prostate cancer biomarkers, the information was scattered across multiple publications in unstructured formats. ProCanBio was developed to consolidate this information into a single user-friendly resource. --- # Objectives The study aimed to: - Develop a manually curated prostate cancer biomarker database- Consolidate biomarker information from published literature- Provide detailed annotations for each biomarker- Develop advanced search and browsing tools- Facilitate biomarker research and validation --- # Data Collection Two PubMed keyword searches were performed: 1. `"prostate cancer" AND biomarkers`2. `"prostate cancer" AND signatures` ## Literature Statistics | Description | Count ||---|---|| Total publications retrieved | 4045 || Duplicate publications removed | 112 || Publications manually curated | 412 | The curated information was extracted manually from published articles. --- # Database Statistics ## Total Entries | Category | Count ||---|---|| Total biomarker entries | 2053 || Unique biomarkers | 1497 | --- # Biomolecule Distribution | Biomolecule Type | Count ||---|---|| Protein biomarkers | 766 || RNA biomarkers | 488 || miRNA biomarkers | 261 || Metabolite biomarkers | 122 || DNA biomarkers | 19 | --- # Biomarker Basis | Biomarker Basis | Count ||---|---|| Expression-based | 1286 || Concentration-based | 378 || Methylation-based | 218 || Mutation-based | 157 | --- # Source of Biomarkers | Source | Count ||---|---|| Tissue | 1069 || Serum | 354 || Blood | 245 || Urine | 170 || Plasma | 137 || Cell lines | 51 | --- # Types of Biomarkers The database contains: - Diagnostic biomarkers- Prognostic biomarkers- Predictive biomarkers ## Major Uses ### Diagnostic Biomarkers Used for distinguishing: - Prostate cancer- Healthy controls- BPH- PIN- Prostatitis ### Prognostic Biomarkers Used for: - Gleason score prediction- Metastasis prediction- Survival analysis- Biochemical recurrence prediction ### Predictive Biomarkers Used for: - Therapy response prediction- Drug response analysis --- # Top Biomarkers in ProCanBio | Biomarker | Biomolecule | Number of Studies ||---|---|---|| PCA3 | mRNA/Protein | 17 || Ki-67 | Protein | 9 || Prostate Health Index (phi) | mRNA/Protein | 9 || miR-141 | miRNA | 8 || PSA | mRNA/Protein | 5 || PTEN | mRNA/Protein/DNA | 4 | --- # Information Stored for Each Biomarker Each biomarker entry includes: - PubMed ID- Biomarker name- Technical name- Biomolecule type- Biomarker basis- Regulation status- Source of biomarker- Patient cohort- Sensitivity- Specificity- ROC-AUC- Accuracy- p-value- Hazard Ratio (HR)- Odds Ratio (OR)- Experimental methods- Clinical trial information- Degree of validity --- # Web Server Architecture The database was developed using: ## Backend - MySQL v8 ## Frontend - PHP v7- HTML5- JavaScript- CSS3 ## Server - Apache HTTP Server- Linux platform --- # Query and Search Tools ## Keyword Search Allows searching using: - Biomarker name- Biomolecule- PMID- Subjects- Regulation conditions --- ## Complex Search Supports multiple query conditions including: - Biomolecule- Biomarker type- Source- Publication year- Subjects Logical operators supported: - AND- OR- NOT --- ## Browse Tools Users can browse biomarkers based on: - Biomolecule- Biomarker type- Source- Biomarker basis --- # Web Server Features ProCanBio provides: - Advanced keyword search- Complex search queries- Browsing tools- Biomarker cards- Downloadable results- Clinical trial links- GeneCards integration- PubMed integration ## Download Formats - CSV- XLS- PDF --- # Case Studies ## PSMA Biomarker Query The database identified: - 15 unique PSMA entries- Derived from 6 research publications PSMA was mainly used for: - Diagnostic applications --- ## Prognostic Protein Biomarkers after 2015 Complex search identified: - 23 unique prognostic protein biomarkers Important biomarkers included: - WISP1- Ki-67- GLUT1- AZGP1 --- # Applications ProCanBio can be used for: - Biomarker discovery- Cancer genomics research- Proteomics research- Clinical biomarker validation- Drug target analysis- Precision oncology- Prostate cancer diagnostics- Prognostic biomarker analysis --- # Technologies Used - MySQL- PHP- Apache Server- JavaScript- HTML5- CSS3- Manual Literature Curation- Bioinformatics Database Systems --- # Important Findings The study demonstrated that: - Prostate cancer biomarker information is highly scattered- Manual curation significantly improves accessibility- Integrated biomarker databases facilitate cancer research- Multi-omics biomarker resources are highly valuable --- # Conclusion ProCanBio provides a comprehensive manually curated resource for prostate cancer biomarkers. The database integrates: - Genomics- Transcriptomics- Proteomics- Metabolomics- Clinical biomarker information with advanced search and browsing capabilities, making it a valuable resource for prostate cancer research and biomarker discovery. --- # Web Server https://webs.iiitd.edu.in/raghava/procanbio/ --- # Citation Sapra D, Kaur H, Dhall A, Raghava GPS. ProCanBio: a database of manually curated biomarkers for Prostate Cancer. --- # Contact ## Dr. G. P. S. Raghava Email: raghava@iiitd.ac.in Address: Indraprastha Institute of Information Technology Delhi --- # License This project/documentation is intended for academic and research purposes only.
