Gene or probe

Cohort

Query summary

Annotation

Normal

Tumor

Genome distribution

Normal

Tumor

Data

Aim

Epigenetic alterations are a widespread signature of human cancer, including generalized changes in DNA methylation status and variability. Whilst frequently affecting small to large regions of co-localized CpGs (i.e. CpG island shores), non adjacent loci also co-methylate.

To evaluate this phenomenon we carried out a serial correlation analysis on the Infinium 450k array using two independent colon cancer cohorts.

Usage

When queried for a given probename, Corre provides its strong associations (effect size Spearman's rho greater than 0.8) to other probes. To ease data input, Corre allows HUGO gene symbols as input: after selecting a probe and a dataset, press the corre! button to start the analysis.

Corre renders the normal and tumor co-methylation data side by side.

Annotation

Co-methylations can be summarized by either their chromosome or its chromatin color (Ernst's 15 chromatin states segmentation by HMM run in hESC H1).

Bubblecharts represent the log2 fold change (enrichment) of your query's co-methylationsas compared to what would be expected from random sampling from the Infinium 450k background.

Treemaps represent the co-methylations as simple counts. You can browse within the treemap by right-clicking (zooms in) o left-clicking (goes back).

Genome distribution

Circular views depict intra-chromosomal co-methylations in red and trans-comethylations in blue.

Data

Spreadsheets can be downloaded as comma-separated plain text files (CSVs) with header. Each row depicts a co-methylation; annotations refer to the probe your query correlates with.

Data

Colonomics series included primary tumors and their adjacent normal tissue from microsatellite-stable samples at stage II (82 at IIA and 8 at IIB) from patients, 67 males and 23 females, aged 43-86 years (mean 70.37); 20 developed metastasis.

The Cancer Genome Atlas (TCGA) series was composed by 256 primary tumor and 38 adjacent normal samples from the colon adenocarcinoma (COAD) cohort from patients aged 31 to 90 years at diagnosis (mean 65.61), being 141 males, 144 females and one unassigned. Pathologic stages included Stage I (40), Stage II (97), Stage III (75), Stage IV (32); 11 were not available or discrepant. Regarding microsatellite instability, 10 were positive, 65 negative and 181 were either not tested or had an unknown status.

External links

Making off

Corre is built with R/shiny and imports the following R packages:

Contact

Any feedback is welcome! Please contact Izaskun Mallona or Miguel A. Peinado.

Corre was developed at the Miguel A. Peinado's lab. The main focus of our research is the characterization of the molecular mechanisms underlying cancer cell programs and the identification of molecular markers with clinical applications.

Please check more details on the lab and our toolshed at maplab.cat.

We are continuously releasing new epigenetics data visualization and integration tools. You might also like:

  1. Methylation plotter, a web tool for dynamic visualization of DNA methylation data (Source Code for Biology and Medicine 2014, 9:11).
  2. Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer (Epigenetics & Chromatin 2015, 8:22).
  3. The Alu knowledgebase, an ontology of the human Alu repeats. (Journal of Biomedical Informatics 2016, 60:77-83)
  4. Chainy, a QPCR workflow. (Bioinformatics, 2017)
  5. Truke, a tool to reshape structured data and look for gene symbols corrupted by Excel misuse. (BMC Genomics 2017, 18:242)

maplab 2017. Developed by Izaskun Mallona. Logo by Julien Douet.