PUBLICATION
IsomiR Bank: a research resource for tracking IsomiRs
- Authors
- Zhang, Y., Zang, Q., Xu, B., Zheng, W., Ban, R., Zhang, H., Yang, Y., Hao, Q., Iqbal, F., Li, A., Shi, Q.
- ID
- ZDB-PUB-160507-1
- Date
- 2016
- Source
- Bioinformatics (Oxford, England) 32(13): 2069-71 (Journal)
- Registered Authors
- Xu, Bo
- Keywords
- none
- MeSH Terms
-
- Algorithms
- Animals
- Computational Biology/methods*
- Databases, Protein*
- High-Throughput Nucleotide Sequencing
- Humans
- MicroRNAs/genetics*
- Plants/genetics
- PubMed
- 27153728 Full text @ Bioinformatics
Citation
Zhang, Y., Zang, Q., Xu, B., Zheng, W., Ban, R., Zhang, H., Yang, Y., Hao, Q., Iqbal, F., Li, A., Shi, Q. (2016) IsomiR Bank: a research resource for tracking IsomiRs. Bioinformatics (Oxford, England). 32(13):2069-71.
Abstract
: Next-Generation Sequencing (NGS) technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent differences from their corresponding mature reference sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). These isomiRs mainly originate via the imprecise and alternative cleavage during the pre-miRNA processing and post-transcriptional modifications that influence miRNA stability, their sub-cellular localization and target selection. Although several tools for the identification of isomiR have been reported, no bioinformatics resource dedicated to gather isomiRs from public NGS data and to provide functional analysis of these isomiRs is available to date. Thus, a free online database, IsomiR Bank has been created to integrate isomiRs detected by our previously published algorithm CPSS. In total, 2727 samples (Small RNA NGS data downloaded from ArrayExpress) from eight species (Arabidopsis thaliana, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Oryza sativa, Solanum lycopersicum and Zea mays) are analyzed. At present, 308 919 isomiRs from 4706 mature miRNAs are collected into IsomiR Bank. In addition, IsomiR Bank provides target prediction and enrichment analysis to evaluate the effects of isomiRs on target selection.
Availability and implementation IsomiR Bank is implemented in PHP/PERL + MySQL + R format and can be freely accessed at http://mcg.ustc.edu.cn/bsc/isomir/ CONTACTS: : aoli@ustc.edu.cn or qshi@ustc.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping