Interrogation of microRNAs involved in gastric cancer using 5p-arm and 3p-arm annotated microRNAs.
MicroRNAs are derived from endogenous stem-loop precursors, and play important roles in various biological processes. From next-generation sequencing data, it is suggested that both the 5p-arm and 3p-arm of mature miRNAs could be generated from a single miRNA hairpin precursor; however, the current miRNA databases fail to provide comprehensive arm annotation features, which could result in ambiguous and incomplete analyses. In the present report, we have annotated over 99.7% of miRNAs with the correct 5p-arm and 3p-arm features. The length distribution of all annotated miRNAs is around 22 nucleotides; however, the 5p-arm miRNAs seem to be longer than those of the 3p-arm, which is evident in the 23-nucleotide group. Our study effort generates comprehensive miRNA arm-feature annotation which can be utilized for better interrogation of miRNAs. In further analysis of human gastric cancer tissues, we identified 38 down-regulated miRNAs and 22 up-regulated arm-specific miRNAs using this new comprehensives miRNA list.
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, R.O.C. Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei, Taiwan, R.O.C.
Wei-Ting
WT
Kuo
Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, R.O.C.
Meng-Ru
MR
Ho
Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, R.O.C.
Chew-Wun
CW
Wu
Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, R.O.C.
Wen-Liang
WL
Fang
Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan, R.O.C.
Kuo-Hung
KH
Huang
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, R.O.C. Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei, Taiwan, R.O.C. wenlin@ibms.sinica.edu.tw.
Wen-Chang
WC
Lin
D000818:Animals; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000502:physiology*; D013274:Stomach Neoplasms / Q000235:genetics*
D035683:MicroRNAs
3p-arm; 5p-arm; MicroRNA; bioinformatics; gastric cancer