PCRM1exportome: Database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes

Yoonji Lee, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, Nick V. Grishin

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Motivation: The consensus pattern of Nuclear Export Signal (NES) is a short sequence motif that is commonly identified in protein sequences, whether the motif acts as an NES (true positive) or not (false positive). Finding more plausible NES functioning regions among the vast array of consensus-matching segments would provide an interesting resource for further experimental validation. Better defined NES should also allow meaningful mapping of cancer-related mutation positions, leading to plausible explanations for the relationship between nuclear export and disease. Results: Possible NES candidate regions are extracted from the cancer-related human reference proteome. Extracted NES are scored for reliability by combining sequence-based and structure-based approaches. The confidently identified NES candidate motifs were checked for overlap with cancer-related mutation positions annotated in the COSMIC database. Among the ∼700 cancer-related sequences in the COSMIC Cancer Gene Census, 178 sequences are predicted to have possible NES motifs containing cancer-related mutations at their key positions. These lists are organized into our database (pCRM1exportome), and other protein sequences in the human reference proteome can also be retrieved by their UniProt IDs.

Original languageEnglish (US)
Pages (from-to)961-963
Number of pages3
JournalBioinformatics
Volume36
Issue number3
DOIs
StatePublished - Feb 1 2020

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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