MYCbase: a database of functional sites and biochemical properties of Myc in both normal and cancer cells

BMC Bioinformatics. 2017 Apr 28;18(1):224. doi: 10.1186/s12859-017-1652-6.

Abstract

Background: Myc is an essential gene having multiple functions such as in cell growth, differentiation, apoptosis, genomic stability, angiogenesis, and disease biology. A large number of researchers dedicated to Myc biology are generating a substantial amount of data in normal and cancer cells/tissues including Burkitt's lymphoma and ovarian cancer.

Results: MYCbase ( http://bicresources.jcbose.ac.in/ssaha4/mycbase ) is a collection of experimentally supported functional sites in Myc that can influence the biological cellular processes. The functional sites were compiled according to their role which includes mutation, methylation pattern, post-translational modifications, protein-protein interactions (PPIs), and DNA interactions. In addition, biochemical properties of Myc are also compiled, which includes metabolism/pathway, protein abundance, and modulators of protein-protein interactions. The OMICS data related to Myc- like gene expression, proteomics expression using mass-spectrometry and miRNAs targeting Myc were also compiled in MYCbase. The mutation and pathway data from the MYCbase were analyzed to look at the patterns and distributions across different diseases. There were few proteins/genes found common in Myc-protein interactions and Myc-DNA binding, and these can play a significant role in transcriptional feedback loops.

Conclusion: In this report, we present a comprehensive integration of relevant information regarding Myc in the form of MYCbase. The data compiled in MYCbase provides a reliable data resource for functional sites at the residue level and biochemical properties of Myc in various cancers.

Keywords: Cancer; Metabolism; Mutations; Myc; Protein-protein interactions.

MeSH terms

  • Animals
  • Breast Neoplasms / genetics
  • Cell Proliferation
  • Databases, Protein*
  • Humans
  • Mice
  • MicroRNAs / genetics
  • Mutation
  • Neoplasms / genetics*
  • Protein Processing, Post-Translational
  • Proto-Oncogene Proteins c-myc / chemistry*
  • Proto-Oncogene Proteins c-myc / genetics*
  • Proto-Oncogene Proteins c-myc / metabolism

Substances

  • MicroRNAs
  • Proto-Oncogene Proteins c-myc