Computational protocol: Epigenetic silencing of tumor suppressor candidate 3 confers adverse prognosis in early colorectal cancer

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Protocol publication

[…] Primers were designed with NCBI Primer Blast (http://www.ncbi.nlm.nih.gov/tools/primer-blast/), based on Primer 3 Software (Whitehead Institute for Biomedical Research, Cambridge, MA, USA), or provided by Epigenomics AG, Berlin, Germany. Primer sequences are listed in . [...] Bioinformatic data were retrieved from cbioportal.org in accordance with the TCGA publication guidelines [, ]. Receiver operating characteristic (ROC) analysis was performed to optimize the PMR cutoff value which yields the best discrimination between non-neoplastic mucosa, adenoma and tumor samples []. PMR values > 30% were considered as methylated, whereas PMR levels < 30% were classified as unmethylated. Statistical calculations were done with the software Prism 4.0 (GraphPad Software, Inc., La Jolla, USA). IHC stainings from patient tissues were analyzed using SPSS version 20.0 (IBM Corporation, Armonk, NY). All tests were unpaired and two-sided, and p-values < 0.05 were considered significant (*). […]

Pipeline specifications

Software tools Primer-BLAST, cBioPortal, SPSS
Databases TCGA Data Portal
Applications Miscellaneous, qPCR
Diseases Adenoma, Neoplasms, Colorectal Neoplasms