IRNdb: the database of immunologically relevant non-coding RNAs.

Elena Denisenko,Ousman Tamgue,Mumin Ozturk,Reto Guler,Harukazu Suzuki,Frank Brombacher,Daniel Ho,Sebastian Schmeier

doi:10.1093/database/baw138

Elena Denisenko, Ousman Tamgue + Show 6 more

Open Access

https://doi.org/10.1093/database/baw138

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Abstract

MicroRNAs (miRNAs), long non-coding RNAs (lncRNAs) and other functional non-coding RNAs (ncRNAs) have emerged as pivotal regulators involved in multiple biological processes. Recently, ncRNA control of gene expression has been identified as a critical regulatory mechanism in the immune system. Despite the great efforts made to discover and characterize ncRNAs, the functional role for most remains unknown. To facilitate discoveries in ncRNA regulation of immune system-related processes, we developed the database of immunologically relevant ncRNAs and target genes (IRNdb). We integrated mouse data on predicted and experimentally supported ncRNA-target interactions, ncRNA and gene annotations, biological pathways and processes and experimental data in a uniform format with a user-friendly web interface. The current version of IRNdb documents 12 930 experimentally supported miRNA-target interactions between 724 miRNAs and 2427 immune-related mouse targets. In addition, we recorded 22 453 lncRNA-immune target and 377 PIWI-interacting RNA-immune target interactions. IRNdb is a comprehensive searchable data repository which will be of help in studying the role of ncRNAs in the immune system.Database URL: http://irndb.org

Highlights

Rapid development of high-throughput technologies enabled identification of non-coding RNAs as a highly abundant class of transcripts in the pervasively transcribed eukaryotic genome [1]
MiRNAs constitute a family of 22 nucleotides small non-coding RNAs (ncRNAs) that bind to target mRNAs to mediate posttranscriptional repression or degradation of the mRNA [2]
We report the development of IRNdb, the first, to our knowledge, specialized database for immune-related ncRNA in mice, a model organism for the study of the immune system

Summary

Introduction

Rapid development of high-throughput technologies enabled identification of non-coding RNAs (ncRNAs) as a highly abundant class of transcripts in the pervasively transcribed eukaryotic genome [1]. We integrated information on mouse miRNAs, lncRNAs, piRNAs and their immunologically relevant target genes. We combined multiple sources of experimentally supported and predicted miRNA-target interactions, eliminating the user’s need to browse multiple websites and run different computational tools.

Results

Conclusion