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Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers |
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| Authors: | Anneleen Decock Maté Ongenaert Jasmien Hoebeeck Katleen De Preter Gert Van Peer Wim Van Criekinge Ruth Ladenstein Johannes H Schulte Rosa Noguera Raymond L Stallings An Van Damme Geneviève Laureys Joëlle Vermeulen Tom Van Maerken Frank Speleman Jo Vandesompele |
| Institution: | 1. Institute for Human Genetics, UCSF, 513 Parnassus Avenue, Box 0794, San Francisco, CA, 94143-0794, USA 2. The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, 35 Medical Center Way, San Francisco, CA, 94143-0525, USA 3. Department of Epidemiology and Biostatistics, UCSF, 185 Berry Street, Lobby 5, Suite 5700, San Francisco, CA, 94107, USA 4. Department of Bioengineering and Therapeutic Sciences, UCSF, 513 Parnassus Avenue, San Francisco, CA, 94143-0912, USA |
| Abstract: | ChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq quality control and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user's data with ENCODE's large collection of published datasets, performs multi-sample normalization, checks against quantitative PCR-validated control regions, and produces informative graphical reports. CHANCE is available at https://github.com/songlab/chance. |
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