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. 2014 Feb 26:4:4197.
doi: 10.1038/srep04197.

PCMdb: pancreatic cancer methylation database

Gandharva Nagpal  1 , Minakshi Sharma  1 , Shailesh Kumar  1 , Kumardeep Chaudhary  1 , Sudheer Gupta  1 , Ankur Gautam  1 , Gajendra P S Raghava  1
Affiliations

PCMdb: pancreatic cancer methylation database

Gandharva Nagpal et al. Sci Rep. .

Abstract

Pancreatic cancer is the fifth most aggressive malignancy and urgently requires new biomarkers to facilitate early detection. For providing impetus to the biomarker discovery, we have developed Pancreatic Cancer Methylation Database (PCMDB, http://crdd.osdd.net/raghava/pcmdb/), a comprehensive resource dedicated to methylation of genes in pancreatic cancer. Data was collected and compiled manually from published literature. PCMdb has 65907 entries for methylation status of 4342 unique genes. In PCMdb, data was compiled for both cancer cell lines (53565 entries for 88 cell lines) and cancer tissues (12342 entries for 3078 tissue samples). Among these entries, 47.22% entries reported a high level of methylation for the corresponding genes while 10.87% entries reported low level of methylation. PCMdb covers five major subtypes of pancreatic cancer; however, most of the entries were compiled for adenocarcinomas (88.38%) and mucinous neoplasms (5.76%). A user-friendly interface has been developed for data browsing, searching and analysis. We anticipate that PCMdb will be helpful for pancreatic cancer biomarker discovery.

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Figures

Figure 1
Figure 1. Architecture of PCMdb.
Figure 2
Figure 2. Data statistics based on (A) Methylation category, (B) Techniques used to detect methylation, and (C) types of pancreatic cancer subtypes.
See this image and copyright information in PMC

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