Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-Scale interrogation of the colorectal cancer methylome by Illumina HumanMethylation450 array

ABSTRACT: Colorectal cancer is an epigenetically heterogeneous disease, the extent to which is unclear. In this study we interrogate the methylome of 216 unselected colorectal cancers using Illumina HumanMethylation450 arrays, and correlate these data with transcript profiles and exome sequencing analysis to elucidate the degree of epigenetic dysregulation in colorectal cancers.

ORGANISM(S): Homo sapiens

SUBMITTER: Lochlan Fennell

PROVIDER: E-MTAB-7036 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Integrative Genome-Scale DNA Methylation Analysis of a Large and Unselected Cohort Reveals 5 Distinct Subtypes of Colorectal Adenocarcinomas.

Fennell Lochlan L Dumenil Troy T Wockner Leesa L Hartel Gunter G Nones Katia K Bond Catherine C Borowsky Jennifer J Liu Cheng C McKeone Diane D Bowdler Lisa L Montgomery Grant G Klein Kerenaftali K Hoffmann Isabell I Patch Ann-Marie AM Kazakoff Stephen S Pearson John J Waddell Nicola N Wirapati Pratyaksha P Lochhead Paul P Imamura Yu Y Ogino Shuji S Shao Renfu R Tejpar Sabine S Leggett Barbara B Whitehall Vicki V

Cellular and molecular gastroenterology and hepatology 20190405 2

<h4>Background & aims</h4>Colorectal cancer is an epigenetically heterogeneous disease, however, the extent and spectrum of the CpG island methylator phenotype (CIMP) is not clear.<h4>Methods</h4>Genome-scale methylation and transcript expression were measured by DNA Methylation and RNA expression microarray in 216 unselected colorectal cancers, and findings were validated using The Cancer Genome Atlas 450K and RNA sequencing data. Mutations in epigenetic regulators were assessed using CIMP-subt ...[more]

PMID: 30954552

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Project description:BackgroundDNA methylation is indispensible for normal human genome function. Currently there is an increasingly large number of DNA methylomic data being released in the public domain allowing for an opportunity to investigate the relationships between the DNA methylome, genome function, and human phenotypes. The Illumina450K is one of the most popular platforms for assessing DNA methylation with over 10,000 samples available in the public domain. However, accessing all this data requires downloading each individual experiment and due to inconsistent annotation, accessing the right data can be a challenge.DescriptionHere we introduce 'Marmal-aid', the first standardised database for DNA methylation (freely available at http://marmal-aid.org). In Marmal-aid, the majority of publicly available Illumina HumanMethylation450 data is incorporated into a single repository allowing for re-processing of data including normalisation and imputation of missing values. The database is accessible in two ways: (1) Using an R package to allow for incorporation into existing analysis pipelines which can then be easily queried to gain insight into the functionality of certain CpG sites. This is aimed at a bioinformatician with experience in R. (2) Using a graphical interface allowing general biologists to query a pre-defined set of tissues (currently 15) providing a reference database of the methylation state in these tissues for the 450,000 CpG sites profiled by the Illumina HumanMethylation450.ConclusionMarmal-aid is the largest publicly available Illumina HumanMethylation450 methylation database combining Illumina HumanMethylation450 data from a number of sources into a single location with a single common annotation format. This allows for automated extraction using the R package and inclusion into existing analysis pipelines. Marmal-aid also provides a easy to use GUI to visualise methylation data in user defined genomic regions for various reference tissues.

Dataset Information

Genome-Scale interrogation of the colorectal cancer methylome by Illumina HumanMethylation450 array

Publications

Integrative Genome-Scale DNA Methylation Analysis of a Large and Unselected Cohort Reveals 5 Distinct Subtypes of Colorectal Adenocarcinomas.

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