CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts
Po-Jung Huang1,2,3, Hou-Hsien Lin4, Chi-Ching Lee5, Ling-Ya Chiu4, Shao-Min Wu2, Yuan-Ming Yeh3, Petrus Tang2, Cheng-Hsun Chiu3, Ping-Chiang Lyu4,*and Pei-Chien Tsai1,2,3,*
CoMut plot is widely used in cancer research publications as a visual summary of mutational landscapes in cancer cohorts. This summary plot can inspect gene mutation rate and sample mutation burden with their relevant clinical details, which is a common first step for analyzing the recurrence and co-occurrence of gene mutations across samples. The cBioPortal and iCoMut are two web-based tools that allow users to create intricate visualizations from pre-loaded TCGA and ICGC data. For custom data analysis, only limited command-line packages are available now, making the production of CoMut plots difficult to achieve, especially for researchers without advanced bioinformatics skills. To address the needs for custom data and TCGA/ICGC data comparison, we have created CoMutPlotter, a web-based tool for the production of publication-quality graphs in an easy-of-use and automatic manner.
We introduce a web-based tool named CoMutPlotter to lower the barriers between complex cancer genomic data and researchers, providing intuitive access to mutational profiles from TCGA/ICGC projects as well as custom cohort studies. A wide variety of file formats are supported by CoMutPlotter to translate cancer mutation profiles into biological insights and clinical applications, which include Mutation Annotation Format (MAF), Tab-separated values (TSV) and Variant Call Format (VCF) files.
In summary, CoMutPlotter is the first tool of its kind that supports VCF file, the most widely used file format, as its input material. CoMutPlotter also provides the most-wanted function for comparing mutation patterns between custom cohort and TCGA/ICGC project. Contributions of COSMIC mutational signatures in individual samples are also included in the summary plot, which is a unique feature of our tool.
CoMutPlotter is freely available at http://tardis.cgu.edu.tw/comutplotter.
Keywords Cancer Mutational Profile Mutational Signature TCGA
Figure 1 – Framework of CoMutPlotter.
In addition to TCGA/ICGC data, CoMutPlotter can take mutational profiles from custom projects in MAF, TSV and VCF formats. CoMutPlotter consists of three major parts: 1) Data input, 2) pre-loaded TCGA/ICGC database, and 3) Output. The output part can be further divided into three panels, which includes the “CoMut Plot” panel, the “Cross-project comparison” panel and the “Download & Report Generation” panel.