Welcome to the official repository for PCMdb, a comprehensive and manually curated database dedicated to DNA methylation in pancreatic cancer. This resource was developed to support researchers working in cancer biology, epigenetics, biomarker discovery, bioinformatics, and translational oncology.
Web Server: http://crdd.osdd.net/raghava/pcmdb/
Nagpal, G., Sharma, M., Kumar, S., Chaudhary, K., Gupta, S., Gautam, A., & Raghava, G. P. S. (2014).
PCMdb: Pancreatic Cancer Methylation Database.
Scientific Reports, 4, 4197.
https://doi.org/10.1038/srep04197
https://doi.org/10.5281/zenodo.20068623
PCMdb is a specialized repository that provides experimentally validated methylation information for genes associated with pancreatic cancer. The database consolidates methylation studies from published literature into a single platform to facilitate biomarker discovery and cancer research.
The database integrates information related to:
- DNA methylation status
- Pancreatic cancer subtypes
- Tissue and cell line data
- Experimental techniques
- Drug resistance associations
- Biomarker information
Data was manually curated from published research articles and integrated with external biological resources.
- 65,907 total entries
- 4,342 unique genes
- Data compiled from 109 research articles
- Includes:
- 53,565 cell line entries
- 12,342 tissue sample entries
- Covers 88 pancreatic cancer cell lines
- Covers 3,078 tissue samples
The database classifies methylation data into five categories:
- High methylation
- Intermediate methylation
- Low methylation
- Altered methylation
- Not known
Approximately:
- 47.22% entries show high methylation
- 10.87% entries show low methylation
PCMdb includes methylation information for multiple pancreatic cancer subtypes including:
- Adenocarcinoma
- Intraductal Papillary Mucinous Neoplasms (IPMN)
- Endocrine pancreatic cancers
- Mucinous neoplasms
Most entries are associated with adenocarcinoma.
The database contains methylation data generated using multiple experimental methods such as:
- Methylated CpG Island Amplification and Microarray (MCAM)
- Methylation Specific PCR (MSP)
- Bisulphite Sequencing
- HRM
- Differential Methylation Hybridization (DMH)
MCAM represents the majority of the entries.
PCMdb integrates several bioinformatics tools to assist users in sequence and methylation analysis:
- BLAST Search
- Smith-Waterman Alignment
- SRS Mapping Tool
- Contig Analysis Tool
These tools help users perform:
- Sequence alignment
- Similarity searching
- NGS read mapping
- Gene prediction analysis
The database provides:
- Keyword Search
- Advanced Search
Users can perform complex queries using logical operators such as:
- AND
- OR
- LIKE
PCMdb allows browsing based on:
- Gene names
- Cell lines
- Methylation category
- Experimental techniques
- Chromosome information
PCMdb integrates methylation data with drug sensitivity information from:
- CancerDR
- CCLE (Cancer Cell Line Encyclopedia)
This integration supports studies on:
- Chemotherapeutic response
- Drug resistance biomarkers
- Precision oncology research
PCMdb can be used for:
- Pancreatic cancer biomarker discovery
- Epigenetics research
- Cancer methylation analysis
- Drug sensitivity studies
- Biomarker validation
- Translational oncology
- NGS data analysis
- Precision medicine research
PCMdb was developed using:
- Apache Server
- MySQL Relational Database
- HTML
- PHP
- JavaScript
- PERL
The platform provides a user-friendly web interface for efficient data retrieval and analysis.
The database is freely available for academic and research use.
Database URL:
http://crdd.osdd.net/raghava/pcmdb/
Indraprastha Institute of Information Technology Delhi
Email: raghava@iiitd.ac.in
This work is licensed under the
Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License
The authors acknowledge support from:
- Council of Scientific and Industrial Research (CSIR)
- Department of Biotechnology (DBT)
- Government of India
We also acknowledge all researchers whose published methylation studies contributed to the development of PCMdb.