PCMdb – Pancreatic Cancer Methylation Database

PCMdb

:: DESCRIPTION

PCMdb is a database of methylated genes found in pancreatic cancer cell lines and tissues. In other words, it provides comprehensive information about methylation status of various genes in Pancreatic Cancer (PCa) and their comparison with transcriptomics and genomics landscape. It is a manually curated database where information is collected and compiled from literature/databases. This database will be very useful to discover novel biomakers for PCa as well as to understand the role of methylation in drug resistance.

::DEVELOPER

PCMdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

PCMdb: pancreatic cancer methylation database.
Nagpal G, Sharma M, Kumar S, Chaudhary K, Gupta S, Gautam A, Raghava GP.
Sci Rep. 2014 Feb 26;4:4197. doi: 10.1038/srep04197.

MLDA 2.0 – Methylation Linear Discriminant Analysis

MLDA 2.0

:: DESCRIPTION

MLDA (Methylation Linear Discriminant Analysis)is a method to identify the differentially methylated loci on CpG island array using Differential Methylation Hybridisation(DMH). It utilizes linear regression models of non-normalised hybridisation data to define methylation status. Log-transformed signal intensities of unmethylated controls on the microarray are used as a reference. The signal intensities of DNA samples digested with methylation sensitive restriction enzymes and mock digested are then transformed to the likelihood of a locus being methylated using this reference. We tested the ability of MLDA to identify loci differentially methylated as analysed by DMH between cisplatin sensitive and resistant ovarian cancer cell lines. MLDA identified 115 differentially methylated loci and 23 out of 26 of these loci have been independently validated by Methylation Specific PCR and/or bisulphite pyrosequencing.

::DEVELOPER

Dr. Wei Dai

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MLDA

:: MORE INFORMATION

Citation

Wei Dai et al.
Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands
BMC Bioinformatics 2008, 9:337

Bis-SNP 0.82.2 – Bisulfite Space Genotyper & Methylation Caller

BisSNP 0.82.2

:: DESCRIPTION

BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol.

::DEVELOPER

USC Epigenome Center

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • java
  • perl 

:: DOWNLOAD

 Bis-SNP

:: MORE INFORMATION

Citation

Genome Biol. 2012 Jul 11;13(7):R61. [Epub ahead of print]
Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data.
Liu Y, Siegmund KD, Laird PW, Berman BP.