ArticlePeerJ2015
miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data.
Article in PeerJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Pseudouridine guides germline small RNA transport and epigenetic inheritance.Nature structural & molecular biology · 2025Article
- MBNL splicing factors regulate the microtranscriptome of skeletal muscles.Nucleic acids research · 2024Article
- Comprehensive profiling of rRNA-derived small RNAs inMethodsX · 2024Article
- MicroRNA Databases and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Extracellular microRNA 3' end modification across diverse body fluids.Epigenetics · 2021Article
- MEF2C shapes the microtranscriptome during differentiation of skeletal muscles.Scientific reports · 2021Article
- IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.BMC bioinformatics · 2021Article
- isomiRs-Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them?Biomolecules · 2020Review
- The epitranscriptome landscape of small noncoding RNAs in stem cells.Stem cells (Dayton, Ohio) · 2020Review
- Article
- Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway.Methods (San Diego, Calif.) · 2019Review
- Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice.Current genomics · 2018Article
- Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice.Journal of integrative bioinformatics · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5' and 3' miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.