FAQ: Frequently asked questions about this server.
1. What are MicroRNAs?
MicroRNAs constitute a recently discovered class of non-coding RNAs that play key roles in the regulation of gene expression. Acting at the post-transcriptional level, these fascinating molecules may fine-tune the expression of as much as 30% of all mammalian protein-encoding genes. Mature microRNAs are short, single-stranded RNA molecules approximately 22 nucleotides in length. MicroRNAs are sometimes encoded by multiple loci, some of which are organized in tandemly co-transcribed clusters.
Figure 1, Overview of microRNA processing in animals, from transcription to the formation of the effector complex. There are two pathways, one for microRNAs from independent genes and one for intronic microRNAs. Enzymes in the picture: Drosha, Pasha (pri-miRNA pre-miRNA) Spliceosome (pre-mRNA intron lariat) Debranching enzyme (intron lariat RNA that can fold into pre-miRNA) RAN-GTP, Exportin-5 (export from nucleus) Dicer (pre-miRNA miRNA) Abbrevations: pri-miRNA = primary microRNA transcript pre-mRNA = precursor messenger RNA pre-miRNA = precursor microRNA miRNA = microRNA miRNA* = antisense microRNA miRNP = microRNA ribonucleoprotein.
MicroRNA genes are transcribed by RNA polymerase II as large primary transcripts (pri-microRNA) that are processed by a protein complex containing the RNase III enzyme Drosha, to form an approximately 70 nucleotide precursor microRNA (pre-microRNA). This precursor is subsequently transported to the cytoplasm where it is processed by a second RNase III enzyme, DICER, to form a mature microRNA of approximately 22 nucleotides ( Figure 1 ). The mature microRNA is then incorporated into a ribonuclear particle to form the RNA-induced silencing complex, RISC, which mediates gene silencing.
See details in (https://en.wikipedia.org/wiki/MicroRNA)
2. What are endogenous and exogenous microRNAs?
Although most miRNAs regulate gene expression intracellularly(Endogenous microRNAs), extracellular miRNAs(Exogenous microRNAs) have been observed in many body fluids. Until recently, miRNA transfer studies have focused on endogenous transfer within an organism, but a report suggested exogenous miRNAs are acquired from dietary consumption. This was the first report to indicate that there may be cross-kingdom regulation from dietary-derived miRNAs and sparked intense specialist and lay interest. Small RNA sequencing as the most widely-used tool for microRNA discovery has now played an emerging role in exogenous microRNA detection. Although challenging, it has great potential to provide evidence of cross species transport in an efficient quantitative manner. Here we present miRDis, a new pipeline for both endogenous and exogenous microRNA analysis based on deep sequencing data.
3. What are isomiR microRNAs?
In the past it had always been said that the same miRNA precursor generates the same miRNA sequences.
However, the advent of deep sequencing has now allowed researchers to detect a huge variability in miRNA biogenesis, meaning that from the same miRNA precursor many different sequences can be generated potentially have different targets. It has been found that isomiR expression profiles can also exhibit race, population, and gender dependencies.
There are four main variation types:
5' trimmingthe 5' dicing site is upstream or downstream from the reference miRNA sequence.
3' trimmingthe 3' dicing site is upstream or downstream from the reference miRNA sequence.
3' nucleotide additionnucleotides added to the 3' end of the reference miRNA.
nucleotide substitutionnucleotides changes from the miRNA precursor. It is thought that may be similar process than post-transcriptional modifications. In the server, we can fiter them out by mature info score(less than 100) and further distingush their types by click the mapped region link to mapping detail.
4. Where can I get the algorithm parameters for my submitted job?
All the algorithm parameters can be found in the top of the results which are ready for download on the left-upper corner.
5. What are the performances of your analyses functions compared to other programs?
| miRDis | CAP-miRSeq | omiRAS | chimira | |
|---|---|---|---|---|
| version | v1.0 | v1.1 | 12/2013 | V1.0 |
| Aligner | bowtie | bowtie | bowtie | blastn |
| Ref Genome | hg19 | hg19 | hg19 | hg19 |
| Time single | 2hr | 5 hrs | 3 hrs | 1hr |
| Down-regulated/Mature(>=5) | 676/879(77%) | 354/769(46%) | 362/692(52%) | 477/913(52%) |
| Down-regulate/Novel miRNA(>=5) | 185/304 (60.8%) | 183/353 (51.8%) | 145/262(55%) | NA |
| Up-regulated/Non-coding RNA(>=5) | 397/544(72%) | NA | 474/581(81%) | NA |
7. How to cite your papers?
Please cite the following two papers if you use our server: (http://sbbi-panda.unl.edu/miRDis)
(i)Zhang, Hanyuan, Bruno Vieira Resende e Silva, and Juan Cui. "miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis." Briefings in Bioinformatics (2017): bbw140.