Infer iRNA expression scores for 11 cancer types
MethCORR is an algorithm to calculate inferred RNA (iRNA) expression scores from DNA methylation β-values generated by the Infinium® HumanMethylation450 BeadChip (“450K”).
MethCORR was established by analysis of genome-wide correlations between gene expression and DNA methylation data for eleven cancer types of The Cancer Genome Atlas (TCGA) program.
RNA expression and DNA methylation data was acquired from the UCSC XENA database as “gene expression RNAseq IlluminaHiSeq" and "Methylation450k", respectively.
The included 11 cancer types are:
- BLAD (Bladder Urothelial Carcinoma)
- BRCA (Breast Invasive Carcinoma)
- ESCA (Esophageal Carcinoma)
- COREAD (Colorectal Adenocarcinoma)
- LUAD (Lung Adenocarcinoma)
- LUSC (Lung Squamous Cell Carcinoma)
- PRAD (Prostate Adenocarcinoma)
- KIRC (Kidney Renal Clear Cell Carcinoma)
- SKCM (Skin Cutaneous Melanoma)
- STAD (Stomach Adenocarcinoma)
- UCEC (Uterine Corpus Endometrial Carcinoma)
Download R-workspace including example data
MethCORR is distributed as an R workspace encompassing all data objects and scripts needed to calculate iRNA expression scores from any user provided 450K DNA methylation dataset of β-values.
Instructions and example data are included in the download file.
The MethCORR software is free for both academic and commercial use. Modification or redistribution of the software is not allowed.
When publishing scientific results, where MethCORR software has been used, please cite the original articles.
MethCORR version 1.00 was developed and tested using R version 4.0.0, the “data.table” R package version 1.12.8 and the “impute” R package version 1.62.0.
Instructions for use are included with the zip download archive.
If you have any further questions, comments or feedback, we are happy to give e-mail support (within a few days) at firstname.lastname@example.org.
MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer.
Mattesen TB, Rasmussen MH, Sandoval J, Ongen H, Árnadóttir SS, Gladov J, Martinez-Cardus A, Castro de Moura M, Madsen AH, Laurberg S, Dermitzakis ET, Esteller M, Andersen CL, Bramsen JB.
Nat Commun. 2020 Apr 24;11(1):2025. doi: 10.1038/s41467-020-16000-6. PubMed
Publisher Correction: MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer.
Mattesen TB, Rasmussen MH, Sandoval J, Ongen H, Árnadóttir SS, Gladov J, Martinez-Cardus A, de Moura MC, Madsen AH, Laurberg S, Dermitzakis ET, Esteller M, Andersen CL, Bramsen JB.
Nat Commun. 2020 Jun 3;11(1):2880. doi: 10.1038/s41467-020-16538-5. PubMed
MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples.
Mattesen TB, Andersen CL, Bramsen JB.
Clin Epigenetics. 2021 Jan 28;13(1):20. doi: 10.1186/s13148-021-01000-0. PubMed