Download and Check the official demo input.

Introduction

The 'Signature' visualization is wildly used in mutational signature analysis. It shows the signature profile with the conventional 96 mutation type classification. The classification first divides mutations into six substitution subtypes, namely C>A, C>G, C>T, T>A, T>C, and T>G. Subsequently, taking the information from the 5' to 3' adjacent bases leads to said 96 possible mutation types. Moreover, we compare each signature with all recorded signature references in the COSMIC database by the cosine similarity test. The top three similar signature references are listed with their percentage of similarity. In particular, possible sequencing artifacts in the signature references are shown in pink while others in blue.

Signature Data (CSV file)

The uploaded CSV file must match the required format as specified below.
Check the official demo input here.

  • header
    The first line of the file should be a header that contains column names as keys. The header should follow the following format:
types subtypes signature 1 signature 2 signature 3 signature 4 signature 5
C>A ACA 0.000353018 0.000284683 0.000401966 0.002938016 0.002984077
  • types and subtypes respectively stand for the six substitution subtypes and the adjacent bases. The values of the two keys should also follows the format shown above.
  • signature 1 to signature 5 each stands for a signature. The name, such as signature 1, is not fixed and can be replaced by any other text. The number of signatures is not limited.

    • rows
      Each row in the file is one of the 96 mutation types.

Display Interactions

There are three types of interactions: Highlights, External link and Download.

  • Highlights
    When the mouse moves on the signature profile, the corresponding bin will be highlighted. Also, when the mouse moves on the three most similar signature references, the corresponding reference label will be highlighted.
  • External link
    Each reference label links to the COSMIC SBS Signatures search webpage.
  • Download
    One SVG file will be generated when the 'Download' button is clicked.

Sidebar Functions

The sidebar provides options to manage files.

  • Files
    • Manage Files: checklist of CSV files uploaded previously, delete or download the CSV files.
    • Upload: upload Signature CSV file. Note that the duplicated file name will be alerted and given a random postfix.
    • Choose: choose files uploaded previously. Note that this function is ONLY available to registered users (each account has certain storage).
    • File Sets: NOT available to this page.

Manual version=1.1, written by Miss. LI Shiying and Dr. JIA Wenlong on 2020-02-03.

  1. Alexandrov, L., Nik-Zainal, S., Wedge, D. et al. (2013). Signatures of mutational processes in human cancer. Nature, 500(7463), pp.415-421. (PMID: 23945592, See Figure 2)
  2. Zhang, L., Zhou, Y., Cheng, C., Cui, H., Cheng, L., Kong, P., ... & Wang, F. (2015). Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma. The American Journal of Human Genetics, 96(4), 597-611. (PMID: 25839328, See Figure 1A)
  3. Li, X., Wu, W. K., Xing, R., Wong, S. H., Liu, Y., Fang, X., ... & Zhou, Y. (2016). Distinct subtypes of gastric cancer defined by molecular characterization include novel mutational signatures with prognostic capability. Cancer research, 76(7), 1724-1732. (PMID: 26857262, See Figure 1B)
  4. Li, X. C., Wang, M. Y., Yang, M., Dai, H. J., Zhang, B. F., Wang, W., ... & Zhang, W. (2018). A mutational signature associated with alcohol consumption and prognostically significantly mutated driver genes in esophageal squamous cell carcinoma. Annals of Oncology, 29(4), 938-944. (PMID: 29351612, See Figure 2B)
  5. Lin, D. C., Meng, X., Hazawa, M., Nagata, Y., Varela, A. M., Xu, L., ..., Loh K. S. and Koeffler H. P. (2014). The genomic landscape of nasopharyngeal carcinoma. Nature Genetics, 46(8), 866. (PMID: 24952746, See Supplementary Figure 3b)
  6. Fujimoto, A., Furuta, M., Totoki, Y., Tsunoda, T., Kato, M., Shiraishi, Y., ... & Gotoh, K. (2016). Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nature genetics, 48(5), 500. (PMID: 27064257, See Figure 2a)
  7. Chang, J., Tan, W., Ling, Z., Xi, R., Shao, M., Chen, M., ... & Xia, Y. (2017). Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations. Nature communications, 8, 15290. (PMID: 28548104, See Figure 1b)

Version

v1.0.1 (2019-12-20)

Developer

Mr. LI Hechen (GitHub)
Miss. LI Shiying (GitHub)

Designer

Dr. JIA Wenlong (Scholar, ORCID, GitHub)

Updates

v1.0.1

  • fix giving random file name when downloading data.
  • add light theme.

v1.0.0

  • initial functions implemented.
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