CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts
Abstract Background 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 t...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-07-01
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| Series: | BMC Medical Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12920-019-0510-y |
| _version_ | 1818570291810402304 |
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| author | Po-Jung Huang Hou-Hsien Lin Chi-Ching Lee Ling-Ya Chiu Shao-Min Wu Yuan-Ming Yeh Petrus Tang Cheng-Hsun Chiu Ping-Chiang Lyu Pei-Chien Tsai |
| author_facet | Po-Jung Huang Hou-Hsien Lin Chi-Ching Lee Ling-Ya Chiu Shao-Min Wu Yuan-Ming Yeh Petrus Tang Cheng-Hsun Chiu Ping-Chiang Lyu Pei-Chien Tsai |
| author_sort | Po-Jung Huang |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions 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. |
| first_indexed | 2024-12-14T06:58:43Z |
| format | Article |
| id | doaj.art-9c1421b35b484d7890915136fdd832c6 |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-12-14T06:58:43Z |
| publishDate | 2019-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-9c1421b35b484d7890915136fdd832c62022-12-21T23:12:31ZengBMCBMC Medical Genomics1755-87942019-07-0112S51710.1186/s12920-019-0510-yCoMutPlotter: a web tool for visual summary of mutations in cancer cohortsPo-Jung Huang0Hou-Hsien Lin1Chi-Ching Lee2Ling-Ya Chiu3Shao-Min Wu4Yuan-Ming Yeh5Petrus Tang6Cheng-Hsun Chiu7Ping-Chiang Lyu8Pei-Chien Tsai9Department of Biomedical Sciences, Chang Gung UniversityInstitute of Bioinformatics and Structural Biology, National Tsing Hua UniversityDepartment and Graduate Institute of Computer Science and Information Engineering, Chang Gung UniversityInstitute of Bioinformatics and Structural Biology, National Tsing Hua UniversityGraduate Institute of Biomedical Sciences, College of Medicine, Chang Gung UniversityGenomic Medicine Core Laboratory, Chang Gung Memorial HospitalGraduate Institute of Biomedical Sciences, College of Medicine, Chang Gung UniversityGenomic Medicine Core Laboratory, Chang Gung Memorial HospitalInstitute of Bioinformatics and Structural Biology, National Tsing Hua UniversityDepartment of Biomedical Sciences, Chang Gung UniversityAbstract Background 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. Results 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. Conclusions 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.http://link.springer.com/article/10.1186/s12920-019-0510-yCancer mutational profile mutational signature TCGA |
| spellingShingle | Po-Jung Huang Hou-Hsien Lin Chi-Ching Lee Ling-Ya Chiu Shao-Min Wu Yuan-Ming Yeh Petrus Tang Cheng-Hsun Chiu Ping-Chiang Lyu Pei-Chien Tsai CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts BMC Medical Genomics Cancer mutational profile mutational signature TCGA |
| title | CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts |
| title_full | CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts |
| title_fullStr | CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts |
| title_full_unstemmed | CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts |
| title_short | CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts |
| title_sort | comutplotter a web tool for visual summary of mutations in cancer cohorts |
| topic | Cancer mutational profile mutational signature TCGA |
| url | http://link.springer.com/article/10.1186/s12920-019-0510-y |
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