Journal article

Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes

Funan He, Ran Wei, Zhan Zhou, Leihuan Huang, Yinan Wang, Jie Tang, Yangyun Zou, Leming Shi, Xun Gu, Melissa J Davis, Zhixi Su

SCIENTIFIC REPORTS | NATURE PUBLISHING GROUP | Published : 2019

Abstract

RNA secondary structure may influence many cellular processes, including RNA processing, stability, localization, and translation. Single-nucleotide variations (SNVs) that alter RNA secondary structure, referred to as riboSNitches, are potentially causative of human diseases, especially in untranslated regions (UTRs) and noncoding RNAs (ncRNAs). The functions of somatic mutations that act as riboSNitches in cancer development remain poorly understood. In this study, we developed a computational pipeline called SNIPER (riboSNitch-enriched or depleted elements in cancer genomes), which employs MeanDiff and EucDiff to detect riboSNitches and then identifies riboSNitch-enriched or riboSNitch-dep..

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University of Melbourne Researchers

Grants

Awarded by National Key Research and Development Program of China


Awarded by National Natural Science Foundation of China


Funding Acknowledgements

All primary data were accessed from The Cancer Genome Atlas Research Network (cancergenome.nih.gov) and International Cancer Genome Consortium (dcc. icgc. org). We would like to thank Wei Huang from Gu lab for his assistance in setting up high performance computing infrastructure. This work was supported by grants from the National Key Research and Development Program of China (2017YFC0908600), the National Natural Science Foundation of China (31771408).